While I understand the "awkward" and "not where we are used to it being" arguments, I do not think that is the main issue with the magnasave on this game. I'm pretty sure the low percentage of saves has more to do with magnet placement and/or strength than it does with button placement. I had a number of games where my hand was hovering over the button, hit it at exactly the "right" time, and watched the ball fly down the outlane anyway. It simply is no where near as effective as the ones on the original BK or any other magnasave game that I have played (and I've played most if not all of them). I'm still glad they brought the feature back, and it in no way ruins the game for me, but it's a bit of a bummer. I hold out some hope that the power can be tweaked in future code that will help, but I'm not holding my breath.
As for the drilling issue...if it were me I would definitely try simulating it with a temporary fix before drilling my cab. I'm sure you could rig up some sort of simple "stick on" button rig and run the wires through the coin door or the vent holes in the bottom. That way you can see if it helps timing, and get the position just right before making sawdust.
My hunch, it will increase magnasave effectivity by exactly 0%. I'd like to be wrong though. I am also in the camp that would be concerned about resale value. Even if done "right" and looking factory, I'm not sure I would want that kind of permanent change on a game I am buying. If done sloppy or if it is awkward with the artwork, even worse. At least keep it within the area a lollipop rail would cover.
All just my opinion though...I firmly believe that if it's your game, you should do what you want to get the most enjoyment out of it. Just be aware the next potential owner might not agree and that may affect the value. Most mod choices are easy to reverse if that's the case. This one, not so easy.