They should provide tools that run in both Windows and plain MS-DOS / FreeDOS (hey, sometimes it's useful). One way I know how to do this is to compile with http://www.delorie.com/djgpp/ and link in the CWSDPMI DOS extender from http://homer.rice.edu/~sandmann/cwsdpmi/index.html

The DOS extender will not run if it detects DPMI provided by Windows, so the binaries work in both environments.

I suggest this for some Atari 800 utilities I wrote: https://github.com/jhallen/atari-tools