Can EDIF Instantiated Entity be Defined by Subdesign During Compile?

If Quartus is giving you an error for undefined entity for these things in the EDIF file, then I expect what you want to do will work. It would be just like having an .edf or .vqm from a third-party synthesis tool that targeted an Altera device but had a black box for something to be implemented in a source file to be synthesized directly by Quartus. This is typically done for black boxing a megafunction, but it should work for your own custom implementation of these primitives.