Yep, you machinist is correct. I swallowed the beehive spring crap. I fought them for awhile. Then I just stopped using them.
Open the pockets up, get the correct springs and go.
BTW, ask your machinist to go to b3racingengines.com and look over his tech pages. He WILL have to correct your geometry and Mike has the best system I've found.
Your valve train will thank you for correcting the geometry. I never look at getting the sweep centered. I'd rather have the sweep as narrow as I can and not worry about getting it centered. IOW, I'd rather have a .050 wide sweep that's outboard of center a bit than an .080 wide sweep that's centered.