There are few incompatibilities, as far as I know. You can't mix machines (compiler option /Tx86-coff with linker option /machine:arm, but this should be pretty obvious).
Compiler options /Gm and /Gn will change the "decoration" of public symbols, so they might cause problems if linking with the wrong library.
Linker options like /align:#, /driver, /entry, /fixed, /force:multiple, /merge, /noentry, /version, /osversion are best left alone - unless you are very sure what you are doing...
This is all I can think of right now...
Pelle