Hi Paul,
basically, you may be right about the pins on an encoder. But there are also encoders, so you should study the datasheet before use to get one set the pin assignment and on the other hand to learn something about the switching behavior and detents.
As you have noticed, encoders have quite different switching behavior. Your X-Encoder has a ratio of 1: 4, so 4 detections for a pulse. The Y-encoder has a behavior of 1: 1, ie one pulse per detent.
Mobiflight is currently unable to compensate for these differences. But that comes with one of the next updates.
If you had learned a bit about this in the forum, you would have found that you are the first to lose data on encoders. But MobiFlight has a logging function (setting debug), which you can activate.
MF will then display all actions of valid configurations on your encoder. As long as you do not spin faster than the system clock, no impulses should be lost
So I see no need to evaluate the RX / TX line.
If you allegedly lost data, have you ever checked your wiring? Did you wire on a breadboard or did you solder the connections?
To answer your question about the supported encoder types, I can tell you that all common encoders can be used. There were already users who experimented with optical encoders, but the result is not familiar to me at the moment.
I can not confirm that there is a timing bug with MF. Corresponding information from the users is also not available in this regard. Thus, this problem seems to exist only in this form with you.
I can not tell you where to debug what breakpoint. I am not the developer, only ambitious user.
One more thing about your appearance here: You should not assume MobiFlight from the outset, just because something does not work for you, as you think it should work. Experience shows in 99% of cases that the configuration is faulty, the wiring was not properly done (including missing GND connections) or defective components were used. Also ignorance with preconditions or interpolation and other comprehension questions are part of inquiries.
If you think you have to behave like an ax in the woods here, that's up to you, but it requires a lot of tolerance not to write back in the same way.
Please do not get me wrong, but this forum lives from the fact that users here report their problems, certainly also address possible errors, always with the aim of obtaining satisfactory information, so that the problems can be eliminated. But that also depends on the HOW of the lecture. I do not want to go deeper here now and I hope you do not mind my subtle hint.