the win32 and dos projects are greatly different. as masm32, the winasm studio was intentionally designed to develop win32 projects.
this means: masm32 has 32-bit ml and 32-bit linker, commandlines are set to 32-bit mode (/coff), 32-bit linker not able to link 16-bit applications in any way.
generally, 32-bit ml still can make 16-bit objects, but then the source has to have proper model definition inside and command line has to match to the target format.
later to be able support 16-bit applications winasm studio have including some options, particulary, it is neccessary to add 16-bit linker as "link16.exe" into masm32\bin folder, but it have dramatically different commandline fomat, thus not all it's options are in use.
finally, when neccesary to have code which able to be assembled in both modes the source has to have switching model using conditional assembly - i have no ever done this, so, can not say any more clever