So... can anyone confirm if Brundlefly has hit the target?

Yes I can confirm, for me at least, with non-destructive MIDI editing unchecked, all fresh MIDI data goes into existing clips.

Not that this thread needs any more reasons offered as to why this is a pain (for some of us) -- since what we're really looking for is a solution -- but I also do a lot of copying of clips.  And sometimes I use the Arpeggiator.  If you you bounce to combine them so you can copy to another part of the project, the "arpeggiated" (is that a verb?) notes are all created in the clip -- NOT what I want to happen.

I came across a strange MIDI behavior related to this issue.  I set up the synth parameters with control messages at the start of the midi clip for volume, EQ, FX, etc.   Whenever I start the clip from the beginning it would play through as expected.  But if I start playback in the middle of the clip, for example around the measure I had been editing, it would be all out of wack.  This drove me crazy checking all kinds of settings and looking for hidden control messages.  Then I came across this thread.

It seems that my clip editing had produced a whole bunch of hidden layers, which of course did not contain the beginning setup messages.  After I bounced to clips I can now start playback anywhere in the clip and it will work as expected.  It could be something peculiar with the VST instrument I am using but I thought I would pass this along in case someone else comes across this problem.