I have my own personal mod that replaces random vanilla patches with Infinite Resource versions, I know you stated it's not supported, but I think it could be implemented.
Looking at function "mine_resource" in control.lua starting around line 441 (in my editor as of "version": "0.3.5" of this mod) I think you can easily fix the issue of going beyond the "min_amount" by simply setting 'amount_remaining' to "proto.minimum_resource_amount" if it's below it.
I'll be making this change to my local version of the mod, however I hope that helps you in resolving this bug. As I know my solution that I will be implementing for myself and my friends probably won't take into account of the %yield chance for randomized returns from mining.
EDIT:
I am also enjoying this mod, and AAI: Hauler.