Thanks. I was able to reproduce that.
However, I'm not sure if its an addressable issue. I believe it comes from the fact that the 2 underground entrances were built with opposite directions (because the game engine did not pair them - as described in the issues above - so IMO it didn't force a matching direction that happens when you build both in powered areas). After supplying power they become a pair so engine tries to match the direction for them to work together.
The fact that the game puts the 'input' part always first when there's no valid underground pairing makes it so that one of them will need to change when power comes up - if it was not manually rotated beforehand, after placement..
Did I get it right or was there something else going on?
Trying to come up with potential mitigation:
The question is which direction does the player prefer?
The non-powered one or the powered one? Or the one that was built first ? - I could implement some forceful redirections based on that - but I'm not sure if it would end up being a better experience overall?
What was the overall context (further than just the reproduction context) in which it has annoyed you - what were your intuitive expectations?
Was it the assumption that the belts should be paired up as usually and the other belt should have been an 'output' underground?
Was it blueprinted before they matched - which probably is more annoying - because after placing the build gets messed?
Including a specific item that player can have that places unpowered belt so that it can just match is not a viable option due to confusing clutter.
Let's think about possible mitigation; if not feasible - I'd otherwise call it additional difficulty/frustration and document in the mod description with the conclusion that its better to build in already powered areas or make sure you rotate belts correctly after placement.
EDIT: added to mod description under Known Limitations.