Using RecurrentComplex version 1.4.8.2 for Minecraft 1.12.2, and for some reason, despite me blacklisting both individual structures and all default RecComplex structures, neither option works to disable them. They still get generated regardless. I only want structures I define to generate naturally.

Try copying the structure files from within the reccomplex .jar and put them in your minecraft/structures/inactive folder. This seems to work for me.