Here are things I have heard while waiting for the heads:
"You're better off just putting them back on, if you machine them without doing the block it will cause too much compression and you'll throw a rod"
"Shoulda just put liquid glass in it"
"You need a shim between the head and the block when you change the gasket or it will idle rough"
...anyone know about the last one? I haven't read anything about it in all my research.
if re-surfacing the head increases the compression enough to cause problems they took off too much. just like there is a max allowable flatness limit there is also a max allowable head shaving limit. the machine shop knows this stuff. or they are a really crappy shop.
did they tell you they needed to be shaved?
usually the amount needed is so small it is a non-issue.
some shops do it in house with a flat surface, thick glass, and the correct sand paper. it does not take long.
some dealers do not even send the heads to the machine shop. they just clean them and reinstall them. i HOPE they at least check them for flat!!!!