Tom,
to cut a thread on a shaft the shaft must match exactly the
nominal diameter of the thread and that's the way SE works.
To have a metric thread say M10 to be cut the shaft must
be exact 10mm in diameter. SE will give you the choice
to choose one of the suitable threads that will fit.
For a threaded hole SE combines the drilling of the hole
with cutting the thread in one function. You may, however,
choose to use the cutout function to create the hole
and later on apply the thread. In this case your pre-cut
hole must match exactly the 'internal minor diameter' that
is the second column in holes.txt.
To stay in the picture: for an M10 (coarse) thread the pre-cut
hole must be exact 8.376mm in diameter.
See the description in holes.txt too, especially when ist
comes to tapered threads
dy