When trying to publish a 64-bit application from C:\Windows\System32 folder, application executable is not available in the Publishing GUI of Remote Application Server. However, it is present in that path when navigated to via Windows Explorer.
In order to publish a 64-bit application, path has to be manually changed to C:\Windows\sysnative\%app.exe%
Note: C:\Windows\sysnative\ is a virtual folder, and it won't be seen in Windows Explorer. Path will have to be entered manually.