Well, it's tough to say. If all the diagnostics go pretty well, but you had already temp-sealed it using a block seal, he likely took it down to see if he could find a marginal head gasket or a crack. Once he went in there, he saw it wasn't a gasket, but the machine shop could still find a crack or warped head.
As much as there are shady guys out there, if I understand the posts, you had it sealed but didn't trust it. So he started looking at it, found it sealed, so went deeper to see what was going in so you could trust it. It sounds like he is trying to make sense of what he sees before the heads get back.
BTW how did you fill it with coolant, did you let it get hot with the cap off and let the thermostat open and add more? Did you drill a small hole in the thermostat (not required but surely helps) I am not a guy who "burps" any cooling system unless it has a bleed valve by design, but you have to add more after the thermostat opens.
As this point, if it were me or my customer, I'd do a good valve job with modern valve seals and if marginal, cut the head surface and if needed the exhaust flange surface.
I could be wrong, but my hunch is he is doing it right to make the car reliable
