what you're planning no worse than what everyone else does, but with more benefit, and i'm not complaining.  i'm just adding to the long list of things i'll need to port when i finally upgrade, and making sure that i (and anyone else reading this- it was a frequent question about V3, and V4 forces base Runtime install) know what absolutely needs to be in the main runtime and what doesn't.

but no, you don't have to put the cr2 in the main runtime at all.  that's why it's a  big performance saver.  even if i use only Brad for a month, say, default scene and all, my (personal) copy of Poser will take forever to load because it's got all of the DAZ scripts and morphs and such in that main runtime. and other people's injectors and Readscripts.  before all of that, it loaded in seconds.  i like acquiring morphs.  but because of injectors that need to be in the main runtime, i have to load everyone's morphs each time i start up Poser.
edited to clarify: load as in load with the rest of the main runtime, not load like morphs into a figure, etc.

there's other issues to maintenance, too.

whereas a cr2 is mainly an issue that one time you actually need it.  when you have to load one or another figure anyway.  the main benefit to on-the-fly switching is if you mostly don't know which version you'll want ahead of time.  otherwise, with one cr2, you'll mostly waste time getting to the alternate version when you know you already know you want the other.  

you can save your cr2 yourself, but the more complicated the cr2 in the first place, the more likely something is to just break.  i have a V3 character that's completely broken in the toes.  they flatten when they bend.  i've never touched a rig or the setup room or anything like that in my life.  all i did was inject the particular morph sets i wanted and save a new character.  and, those same morphs are in a different V3 character i saved without any issue.  sometimes i think Poser has some sort of evil gremlin inside of it.