~ diff <(echo format coff > x ; fasm x ; hd x.obj) <(echo format ms coff > y ; fasm y ; hd y.obj)
4c4
< 00000010  00 00 04 01 2e 66 6c 61  74 00 00 00 00 00 00 00  |.....flat.......|
---
> 00000010  00 00 84 01 2e 66 6c 61  74 00 00 00 00 00 00 00  |.....flat.......|
6c6
< 00000030  00 00 00 00 00 00 00 00  60 00 00 00 2e 66 6c 61  |........`....fla|
---
> 00000030  00 00 00 00 00 00 00 00  60 00 00 e0 2e 66 6c 61  |........`....fla|
~    

The most important one is that REL32 relocations are computed differently, compare the implementations in fasmg's coff.inc and coffms.inc.

Also, because Microsoft's variant has been developed further (and into 64-bit world), it has substantially more extensions, additional flags, etc. The basic variant follows the old DJGPP specification.

The $% is a built-in symbol equal to the offset within the output file at which the initialized data would be generated if it was defined at this point. The $%% symbol is the current offset within the output file. These two values differ only when they are used after some data has been reserved - the $% is then larger than $%% by the length of uninitialized data which would be generated into output if it was to be followed by some initialized one.

                start           present*        end
address space   $$              $@              $
output file     0               $%%             $%