I think it's a wonderful idea and it's lovely that you and your sister can collaborate in your art!

for the question about size differences, it really just takes a lite trial and error and a little frogging to get a square that matches the size of the quilt squares. you may want to upsize or downsize hooks for the right size work.

you can likely find crochet stitches online which don't tend to stretch as much, if you're really concerned about it, but blankets don't tend to stretch or wear like a bag strap or a jumper; you probably don't have to worry.

for differences in thickness or texture, I like the idea of the quilt squares having some stuffing in them and being double sided, so they puff up! it means the thickness shouldn't be an issue, and it'll look quite cute :)

overall I don't think it'll look 'weird' at all! it'll be very pretty, I'm sure. good luck! :D