OK, thanks for all the replies, guys. Couple of my thoughts here:
You could have easily changed the time signature to 6/8 without affecting the playback of the MIDI or audio, and then used Set Measure/Beat without bouncing the MIDI. I do it all the time.
My experience differed. Changing the time sig didn't shift anything, true. However, with Set Measure/Beat tempo changes, MIDI clips starting shifting drastically.
Azlow, interesting and I appreciate the work you put into plug-ins, maybe I'll try yours out, but I have to read your page again to really see what it's about.
"Slip Stretch" MIDI clips like we can with audio. Essentially you can hover over the end (or start) of a MIDI clip, hold a binding (Alt IIRC... perhaps Ctrl) then "Slip Edit" it so that the data within "stretches" proportional.
I actually did try this out, but the notes ended up with strange durations, didn't really work. Again, maybe because my recorded tempo vs. actual tempo was so drastically different.
Maybe the take away is to always record to a tempo from the get go?
I think for me, the take away's are two:
1) Set an approximate tempo and time signature even if not recording to a click.
2) Set Measure / Beat tempo mapping BEFORE recording any MIDI tracks.
This works in my client context where I usually record the client's guitar and vocals first, then go back and add MIDI tracks.
The last takeaway really is that even if I think a song recorded in "free time" won't need any timing adjustments after recording additional tracks, it still might, and so planning for it is worth the effort, because it's a royal PIA to sort it out afterwards.