In Deuteronomy, Moses says "For this command that I command you today is not a wonder to you and it is not distant..." I want to explore the (possible) tension between this sentiment and laws whose logic may not be clear to us or where modern understanding changes the original rationale (e.g., using non-porous dishware going against practice of maintaining two sets). I'm sure this has been explored and would just appreciate the best source that lays out the arguments. Thx.
Theoretically it is possible to switch from dairy to meaty utensils every time and perform hagala in between. We don't do it for practical reasons, to avoid mistakes, based on a gemara in Chulin 8b (see here for details).
I don't know if you meant to ask specifically for this or more generally about the fundamental rationale of mitzvot, you might enjoy the following books