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I think I'll definitely leave the toecaps and brows in, but maybe set their "gone" morphs to 1 by default, so one only has to worry about them when they're needed.

Just my .02...
Actually, I hate when a figure has any morph on it set to anything but 0 by default.
When I first got V4 the first thing I started doing was creating new morphs for her. I searched all through the massive set of morphs that came with the original V4 super-megamaxi+++ whatever-it's called bundle for any morphs that were not at 0 and didn't find any. So then I set about creating some FBM's and discovered later that the eyes or corneas, or whatever were set to 1 or negative one. Can't remember now.
But the point is, since I overlooked that I ended with with a few useless FBM's before I discovered it, as the eye morphs were compounded atop the morphs I had made.
If it were me I'd make the morphs and put them in there, but include in the readme how to get them out. When I think how much time I've spent over the years searching through a new figure to make sure every last morph is zeroed and still miss one or two, it's made me very opposed to the idea of any morphs preset in a base figure.