I ride in jodhpur boots most of the time, only putting on tall boots for shows or lessons, and half chaps occasionally for a trail ride (but not always). No problems with rubbing.
I still have a few pairs of functional “On Course Cotton Naturals” but some other new types have elastic at the ankle and fabric all the way down. I have a nice pair from Irideon with ribbed fabric and pockets which are my go-to for trail rides and carrying my phone. Some other cheap pull-ons (Devonaire?) also have the same fabric all the way down. You could also wear socks on the outside of your pants when you have the thinner fabric.