Others will no doubt comment and have slightly different advice .......
FWIW, the sealing relies entirely on the clean surfaces and the nip of the O-ring. The nip depends entirely on the depth of the groove. Because the covers were plastic they were relatively flexible and the outer surface should come down pretty much flat onto the engine casting. As long as the groove depth is consistent the O-ring nip should be consistent and they shouldn't leak.
I wouldn't concern myself particularly with the flatness of the plastic face (unless it's a million miles out, in which case you need another cover), indeed if you take material off in certain areas all you'll end up doing is reducing the groove depth, which could potentially end up with too much nip.
I'm not sure what exact detail the top hats are intended to have regarding upstand or recess. In principle top hat inserts in plastic covers are to enable the fasteners to be tightened enough to stop them coming loose, a softish plastic cover doesn't provide enough strength to give this so a metal insert is used. The inserts are usually designed a fraction short of the plastic depth so it "just" pinches the plastic but without distorting it significantly. Once the mating faces touch the O-ring should have the correct nip to seal, the plastic cover then does not need significant additional clamp load.
If the faces are good, and the groove depth is consistent, personally I would avoid using sealant, it shouldn't need it. If you really do need to use it, I'd recommend something like Loctite 5980 which I've found extremely reliable. Halfords do small tubes of it for around £7.
Other opinions may vary..........
