Vortec heads have 64 cc chambers, not 60-62. Yes you will have a higher compression ratio if you run flat top pistons. As for using a vortec head in a mild rebuild of a 400, I'd still use them. They are way better than the stock heads from that era. Keep the cam tame (under .490" lift) and they will live in stock form. They flow just as good as the old Bow Tie performance heads (unported, stock). So with a dual plane intake, mild (but not wimpy) cam, headers and good exhuast you could have a strong reliable engine with plenty of torque. (keep in mind that the stock Vortec head is what is used on the GM 330 deluxe crate engine, the Ramjet crate and the HT383 crate engine so they can work in higher than stock output applications)
The special intake gaskets are under $30 and they are reuseable so you don't have to pitch them everytime you have to pull the intake. The rockers are of the self guided variety, of which are pretty cheap at the dealer or even cheaper if you scrounge at a machine shop or boneyard (they have been used since the late 80's so it's not just a Vortec thing). As for EGR, if you need one, you can run a port off of your header/manifold to supply the exhaust to it. They are still a bargain even with the special stuff you need to go along with it when comparing to a complete set of aftermarket heads that run at 800-1000 per pair complete or more.
Tim's right if you are going for balls out HP, as much as you can afford. If thats what your goal is and have the funds to do it, get Darts, Worlds or one of the other aftermarket head companies stuff. If all you want is a mild rebuild with reasonable HP/tq levels and the budget's tight, get the vortecs.