I was in a situation where I had to compile the app, modify the (physical) EXE with another app and then add it back into the distribution.
I think Wise (at least the version I had) would require that your modification step be performed before you started packaging. IOW, it had no capability for a "Pre-package" or "Post-package" step to be defined.
If you were modifying the EXE as part of the application (like, tweaking the EXE to insert a serial number or something), Wise does support this, but I've never done it. I think it requires writing a custom "C" Dll to insert your info in the correct spot in the EXE.
Wise has the ability to extend the setup program by writing a "C" DLL, which I've done. Pretty straightforward, and you have access to all the variables in your Wise script. So you potentially have the ability to do nearly anything that can be done from inside a DLL.
Chip H.