Depends on what you mean by manipulate.
You can edit each track individually. Therefore multiple MIDI tracks with same channel doesn't matter from that point of view. Anything you want to do do a track you can, regardless of channel (as far as editing). It won't affect another track with the same channel.

And you can send each track out a different port, so that part doesn't matter either. Each instance of the same MIDI channel can be on a different track and being sent to a different port (or device). In the softsynth world these can even be the same synth!

Example -
Track 1 & 2 have data on the same MIDI channel.

You want to use both tracks for that 'Favorite Best Ever Synth'.
Assign track 1 to DXi/VSTi synth 1 port. Then load that favorite synth on that port.
Then assign track 2 to DXi/VSTi synth 2 port. Load another instance of that favorite synth (so it acts like a totally different synth).

Now you can do anything you want to each track, have it on the same MIDI channel, and be totally independant of each other. Each instance of the synth will only be affected by the data being sent to its port.

This is not best practice, I know. But if you think it through there are a lot of possibilities in the Track-MIDI Channel-Port layering. My point was the tracks (regardless of MIDI channel) can *always* be manipulated without being harder than any other track.
Even if you want to use those 2 tracks on the exact same device you can select both tracks and do the same edit to both tracks at once. I guess I don't see why you say -

"Once data from multiple RB "Midi" TRACKS is recorded to the SAME Midi CHANNEL, I'm guessing it can be harder to manipulate."

If you ever do hit that wall, just use 'Edit-Rechannel MIDI' and change the MIDI channel for a given track.


Make your sound your own!
.. I do not work here, but the benefits are still awesome