Thank you for the thought out reply. I'm with you man. That's why I made that example project that I posted. It's the simplest circumstance under which I could reproduce the exact bug I'm referring to, and I think it illustrates the problem more than adequately. Although it doesn't illustrate the other PDC issues mentioned in this thread.
...the engine needs to delay the audio channel in order to compensate for the extra delay in the AUX channel, but in so doing, wil it also be now sending its own audio even later to the AUX channel through the send?
Right, so that means for every downstream point where the audio signal is split (i.e. sent to an actual output), Logic would have to duplicate the source and entire signal chain thus far, adding a different latency compensation offset according to the latency added prior to that particular juncture. Okay, that's totally untenable.
Instruments could be improved in LogicPro by not using AUX channels for them. They should have a dedicated Instrument extension which are technically not AUX channels, but just multiple instrument outputs on an instrument channel...and then all instrument channels would cause the input midi to be queued earlier as appropriate for any PDC on the instrument channel.
Yeah, that would certainly help but I believe it would require plugin developers to code for that functionality. As in, the plugin would have to tell Logic what MIDI is triggering audio on which outputs in order for Logic to be able to properly move/retime the midi to account for downstream latency.
All of this aside, I am not a DAW designer, I am a musician. As fun a distraction as it is to ponder why it works or doesn't work, it's not our job to figure out how to make it work properly. It's my job to make music, and right now the DAW is hindering my ability to use what I've come to understand is a pretty common workflow. I've done as much as I can to illuminate the issue, short of submitting a bug report I suppose. So I guess that's the next step. Unfortunately it doesn't look like they let you attach a file though, which would be the quickest way to illustrate the issue. That, and they ask you to fill out a survey longer than an online job application.
Genuinely curious, do Apple engineers ever check these forums?