here's another picture - this one, for drum racks:
this is very similar to the above, except that in this case, it's in a drum rack. i just took the standard kit-909 classic from drum machines with a 4/4 pattern, and duplicated the kick chain. the volume shapers are not doing anything (flat) and the reverberate is set to 4096 samples, but 100% dry, so not doing anything but generating latency.
you can again see that the bottom volume shaper is seeing the automation out-of-sync issue (this is actually visible in the scope too - i guess i don't really need the volume shaper - incidentally, i don't know if you can still get oszillos, but volume shaper is also cheap and acts as a single-signal midi-synced scope - great for this!)
in the scope, the top two signals are at the chain, and you can see that there, they aren't in sync.
however, the third (green) signal is where both of them are sent to send, and the scope is the first effect in the send - here, they are synced, so ableton is compensating the send and aligning them. the last one (purple) is the overall output of the drum rack, which is mixing the two separate kicks and the return for the send chain (i reduced it a little bit in the mixer just to make it fit; because we're adding as we go, the bottom waveforms are louder than the bottom ones). and even the overall output of the drum rack is completely in sync.
at least for this simple case... i'd love to do some further testing, if someone has some specific cases where this doesn't work. so far, I've tried mixer sends, the master, and drum rack send/returns (i didn't see instrument send/returns, though i thought it had them?). that's everything i can think of, and at least for the simple cases, the audio is always in sync.
since they already have these values, it looks like each plugin asks the host for timing as it goes; the host needs to respond with a different value for every plugin, and maybe that's the piece of code that needs added.