That's generally the idea to bypass most types of DRM. External/Internal patching is not a new thing. However, even disassemblers still have problems with truly decompiling P-Code, since most of the internal routines are technically "undocumented" and have been for quite some time. More than that, code obfuscation techniques aren't new either, and by definition, anything can be cracked. It just depends on how much work you want to put into it.
As for an API wrapper, considering that most of the code is a direct result of CLI scripting, the actual workaround would be to modify/fake batch scripts on the fly. The only way to do that is to either rewrite portions from the source code itself, or do an internal jump/patch (internal or external, doesn't really matter), which defeats the purpose anyway.