No, there is no bytecode. A legacy mode executable is just a normal EXE as defined by Microsoft. A pure mode lite-C executable however is a normal EXE wrapped around another EXE. It's executed in two steps: the wrapper EXE loads acknex.dll, which performs a self check and then transfers control to the embedded real EXE. This should however normally not matter for protection systems.

But calling the enigma DLL from lite-C is of course the easiest way. Look here:

http://manual.3dgamestudio.net/litec_api.htm

Just put a #define PRAGMA_API definition in your code and then you can call the enigma DLL function.