I am replacing a thruhull that was coupled to a properly backed,
bedded and bolted flanged base seacock.

Question: Do I cut the thruhull exactly to length plus 1/16" so that
it butts to the inside shoulder and leaves a room for a thin pillow of
caulk against the hull?

or Do I cut the thruhull shy and tighten it down just enough to leave
a thin pillow of caulk against the hull?

IMHO. You should cut it slightly short of bottoming out inside the seacock.
A half inch or so of thread engagement is all that is required in pipe
fitting.

When you tighten the valve onto the thruhull, don't make the common mistake
of over tightening. This would squeeze out all of the caulking compound.
You have the correct idea in leaving a think film of sealant between the
thruhull, valve flange and hull.. (in installing deck hardware, etc. I bed
them by only lightly tighening the bolts, I then come back after the sealant
has cured some, hold the bolt and tighten the nut until everything feels
firm. Don't let the bolt turn.)


--
My opinion and experience. FWIW

Steve
s/v Good Intentions