They are going to put new gaskets on it, but I agree with Fredo. If the valve cover is original, have them replace it and ask if you can keep the new gasket that was paid for by warranty that you can sell or keep for a later date.
If the bolt heads are broken and missing they will pull the pan to get them out. Easy money for the tech and they aren't gonna pass that up since warranty should pay for it.
Agreed again with Fredo about the engine mounts but your car doesn't have a rubber steering coupler like the E46 so you should be fine in that regard.