Yo Stellaris devs, questions like this are why the logistical growth system is dumb. If you wanted fewer pops, just cut pop growth. There was no need to obscurely relate it to so many variables, and in the process make managing one's empire even more of a pain.
Ass to your question OP, I seem to remember there being a video knocking around (not from Stefan) where somebody broke down how capacity relates to pop growth. Effectively they disentangled Paradox's mess of bad tooltips. If I'm remembering correctly, the best thing to do is +% pop growth since 1% of pop growth is worth more than the additional capacity of anything other than Ecumenpolis districts. So unless it's an Ecumenpolis, prioritize pop growth before capacity.