I have been repairing electronics/mechanical assemblies for over 25 years and i have developed the following philosophy.
"If a modification is required to fix a problem, then it is not a fix but a design change and that does not end in a quality result." That is my repair philosophy in one line, with that being said engineers are not perfect and defiantly do make mistakes. Those mistakes can become big problems and are well known. For instance we can point to gottllieb system 1 for example of a bad design that requires modification to keep it running, mainly adding grounds to keep the poor grounding choices of the engineers from constantly failing. But also this failing is well known. Down through the years in my repair career engineering departments quite often issue design changes to repair technicians to correct a flaw in the design.
Modification to repair something is not a good choice when you are in a normal repair situation. One Common modification i see is that if you have a bad connector, then solder the wire and bypass the connector. All you are doing is to frustrate the next repair that will need to be made to keep these antiques running well.
If you are making a modification then understand that you are altering the function. For instance on older em pinball machines you need to modify the credit reel to make the game free play, because there is no free play option on all em machines.
So when you are working on your game, ask yourself the following question "am i repairing it or modifying it" Then if you are modifying it, do you understand the ramifications of the modification. This philosophy is not limited to just the electronics or electrical system, this is also true for the playfield and mechanical assemblies. in fact i see more modifications to the mechanical assemblies then electrical. one mechanical alteration i see allot is shorting a spring to repair not modify the function. The common misconception is that the spring is weak. As a general rule this is not true. In most cases it is a mechanical failure that goes undetected by the person repairing the machine. Just because a lever is moving does not mean that it is moving correctly per the design. Just putting oil on a lever that was designed to run dry does not fix the function of that lever it may work better in the short run but it will eventually cause more problems in the future.

"When electronic parts become obsolete and are no longer obtainable, substitutions are necessary, which might not be quite like the original design, such as the replacement bridge rectifiers for classic bally/stern rectifier boards."

nothing is absolute, what I wrote was not meant to be taken like that. When a part becomes obsolete and you need to substitute a part that as long as you understand the effects of using that part it makes sense to make that change. When you start a repair or are working on a repair the idea is to keep it as original as possible.

"When buying pins that were on route, there will inevitably be hacks in there just to keep the machine running, which were not part of the original design."
sure you will find that but it is not a quality repair. I have worked in the field and sometimes you need to get something "working" but I will follow that up with getting the right parts on a return visit.

"Proper fixes cost time and money."
absolutely, quick fixes lead to more trouble in the future, it is not a quality fix done fast an cheap.

"When I swap out an old two prong plug and ground the high voltage on the door and flippers so that someone doesn't land in the hospital from the shock, I consider that repairing the mistakes of those who came before me. Not modifying the game. "

It is a modification, I don't want to deaminize the word modification. If you change the original design no matter how awful the design is it is still a modification. Adding a third prong ground is a
great modification. A modification can be good or bad.
I said "ask yourself if you are making a repair or a modification" - if you are then know it as a modification not a repair.

"In all seriousness, there is a whole mound of repair information around documented suggested fixes/repairs/modifications all kind of lumped together."

yes, and that should concern you, do you know really how it will affect your machine?
it bothers me to see that because people will see it as an absolute "fix"
attempting a modification per instructions on the internet is not always the correct thing to do.
And it is virtually impossible to verify most of the verifications are anecdotal. So you basically need to trust
the poster that he knows what he is doing. and some are very good, some are very poor.

I agree, absolutely but the manufacturer will issue a modification bulletin.
and maybe some are missing my point. A technician out in the field does not have the same
level of information and understanding as the engineer of that product. We can't we weren't included in the design process. We have the schematics and diagrams which only tell half the story. applying my "philosophy" is the best way to head into a repair.
I have worked with many engineers in my career and I can tell you that some of them don't really understand a technicians role very well and can be quite condescending about it. And I think the Designation of who is an engineer has eroded to technicians calling themselves engineers. I have been a technician many years, and when you are working with limited design information you need to stick with the original design until it is impossible to do so. out in the field a technician does not have the luxury learning the details of everything he needs to repair. You are thrown into the fire so to speak needing a quality and successful outcome. my philosophy has served me well to achieve this outcome.

I think we are just mixing semantics here I am glad you had great results but it is bad practice to go into a repair thinking a modification is the correct action to fix a problem. maybe that is a better way to explain it.
the next question to ask is can these modifications be applied to all machines with the same result if you don't have lab testing your reasoning is antidotal only. When I worked in the lab before even the smallest change went out we tested the design fully. Any mod found on the internet will have this same hit and miss reality.

no I am not, example if you have a spring that is not returning like expected do you do you shorten it or try to find out why it will not return correctly. when in the past it worked fine. go into the repair looking for the underlying cause don't just shorten the spring. If the spring is bad then replace it. that is the meaning of that. too many times they will stop short of the real problem where a modification seems to fix the problem. Then you end up fixing it again 6 months later. What I said above is good sense approach to all repairs. I have seen other techs approach a repair where a part is obviously not preforming well, will modify something else to make it work better. This has happened in my profession. I have seen it many times. I will not work like that. Happy customers are important to me. if you want your repairs to hold up to the test of time you need to approach all repairs like this.

if you don't agree fine. my point was to help people in there attempt at repairing an issue.
not to pat myself on the back, just trying to give back a little. I was hoping that my long career and the trials I went through would help somebody else and make it easier for them. if you are unsure how to proceed in a repair don't modify it to fix it.

that is all I have to say about it.
sorry I even tried.