Orel:
I think the notation view is best regarded as a reasonably useful work in progress for now. I don't know what Cockos' priorities are, but hopefully it'll gradually improve as version 6 goes on. Maybe one day we'll get a fully integrated solution.
I tend to split the task into two chunks and use the best tool for each job. That is, I work in Sibelius up to a certain point then export the MIDI into REAPER for really detailed mockup work (and the occasional fix). I actually find this task division a useful workflow anyway - I'm in full-on composing mode in Sib (where things don't need to sound that good) then in full-on programming mode in REAPER (where I'm solely concerned with making things sound as good as possible).
So I don't really use notation in REAPER, but I seem to recall that one of the right-click options in the notation editor is to insert a key change. Presumably that would at least default accidentals to flats or sharps according to the key.
As to the issue of the clef split point, I imagine that's a nightmare to program. It's difficult enough to manage in a dedicated scorewriting/engraving program.
One option would be to have two separate tracks for treble and bass clefs. (I tend to do that anyway, for ease of editing performances and for some simple extra control over low and high end in piano samplers.) But perhaps REAPER would then simply display another staff rather than using leger lines as you wish. Worth a try.
Attached is a script to split a full keyboard track into RH and LH tracks at a user chosen note. It might be useful to you.
https://www.dropbox.com/s/ec82ezg3c1...dAlfa.lua?dl=0
I'll earmark this thread though - maybe someone will come along with better advice.