I am afraid I don't understand. SetupBuilder creates a native setup.exe installation executable for your project(s). It installs your original files (e.g. .exes and .dlls) to the target machine. It does not "modify" your original files (e.g. your DLL) in any way.

SetupBuilder lets you package several DLLs (even with the same name) into the same setup.exe for installation, no problem.