I don't see what the problem is... You can manually export your map to .map file in Hammer or use HLfix to convert it into a .map file.
I said it before and BigD also said it. The compile tools can only compile a map into a .bsp file using the .map file format. The option to compile using a .bsp file is mainly there for light.rad tweaking, so you can simply recompile the lights without having to recompile the csg/bsp and vis parts. That is if you haven't made any architectural changes...
Just simply export your map to a .map file format and you're set to compile it... When you compile with Hammer, as I said, it also converts the file to .map for the compile tools to use. You just don't see this part because its hidden behind a user interface

There is no hocus pocus going on here