What you need is compare the values of pure-bytes-used in "emacs -Q"
between Emacs compiled on Cygwin and on some Unix or GNU system.
(Make sure both builds use the same configuration options and are done
on platforms with the same size of basic data types and of EMACS_INT,
which probably means a 32-bit Unix or GNU system.) Then subtract
these two values and round up.
Another alternative is to run "temacs -batch -l loadup" under GDB, set
a breakpoint in pure_alloc, and record every allocation that comes
from Cygwin-specific code; summing them up should give you the extra.
But this is much more tedious, as you'd have to examine lots of
allocations.