I agree that as long as the truss rod is within its normal range of tightness (that is, not overtightened), you aren't likely to hurt it tweaking it a couple of times a week. If you actually do all that string changing, I think you'd quickly find a compromise setup that would work well with both strings, so you wouldn't really be touching the truss rod that often.
Your bigger problem is going to be wearing out the strings. Flatwounds normally last for years, but if you swap them several times a week, you are going to be replacing them quite often. They don't like to be constantly bent and unbent around posts and through bridges. Roundwounds aren't as fussy, but you will still shorten their life by constantly swapping them.
I think you'll quickly either settle on one or the other type of strings, or get a second bass.