I recently stained a mahogany cold molded boat with aniline dye and it came out fine. I did test for adhesion first with oil based and latex stains......and found that both created problems with epoxy....but the aniline stain didn't noticeably change adhesion.
One caveat....the darker you make the wood, the more you will notice any glass that doesn't get completely wetted out....so be extra careful not to starve the cloth.

: I am just starting to build my first stitch and glue boat. I decided on a
: Pygmy Osprey HP. My first mistake was building a table to work on, it was
: 2 ft to short, Doh! I know this is a premature question, but can one stain
: the wood before you cover the hull in epoxy and fiberglass cloth? Has
: anyone installed the Pygmy hatches and bulkheads? They do not look they
: wood be terribly effective in keeping water out especially if the water is
: rough. Thanks in advance.