Patch files are generated by comparing your versions and generating the smallest possible patch file. That's presuming you follow the instructions (namely: include all files in all versions in wyBuild), and that you don't "bloat" your files with things like obfuscation which increase file size without adding any benefit (really, obfuscation has absolutely no benefit). Generating patches to obfuscated executables are giant compared to patches generated from plain-old compiled files.
Does that make sense?