Welcome!

First rule - "if it ain't broke - don't fix it"!

Is the ball trough giving problems? No, then leave it and move on to better issues that I'm sure you will have.

Those small .100 connectors are rubbish which is why someone has bypassed them by soldering the wires on directly and yes, the emitter board is connected across to the receiver board on these machines just as you have it, albeit usually with a 5 pin connector. They have done this because, very likely, the ball trough was intermittent and causing all sorts of random game issues.

More importantly, those large 2 or 3 watt resistors get SUPER hot and even fall off the board. They cause all manner of issues and you could replace that board with a more modern one that doesn't have this 'hot resistors' issue for only $32 if you really want to improve the reliability of the machine.

https://www.pinballlife.com/7-opto-trough-emitter-board-for-williamsbally-widebody-pinball-machines.html
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