There are various threads about corroded covers being replaced under warranty so presumably the covers and crankcases are not matched (line bored) in the factory. Mine has gone where the belt cover bottom edge has fretted against the timing cover.
Any bearing pocket must be masked. As its an end cover you could** get away with coating the joint face. BUT you will need to make sure the face is flat by rubbing on emery paper over a suitable flat surface. **be absolutely sure the extra mm of coating wont cause problems.
Assuming the cover is not part of the crankcase (see above), coating the gasket face prevents corrosion seeping under the coating from the open edge. Any sharp corners (anywhere) need to be gently radiused or the coating may peel away. Again, the joint face will need to be rubbed level, otherwise the joint will leak.
On mine I did not mask the bolt holes I just drilled out the excess coating leaving a flat face for the bolt heads. I started with a countersink then followed through with a drill and managed to not crack the coating.
My Yamaha crank end covers were coated all over (inside and out). There was no cracking at bolt holes, no corrosion seeping under the joint edge and no oil leaks in the 3 years they were on the bike. There is a risk of bolt pressure cracking the coating so you might want to mask as Al suggests but this does provide an immediate route for corrosion. Slimline copper washers under each bolt head might help to spread the pressure but there is no perfect solution.
Edit - Gasket faces with an O-ring slot MUST NOT be coated. Any coating in the slot is bad news indeed. The Yammie had flat joint faces.
My BMW alternator belt cover seems to have fretted against the front timing cover causing corrosion. Although not in the manual a gasket sealant on the plastic belt cover e.g. Loctite 531 might prevent the fretting. Probably leave a 10mm gap at the bottom to let condensation escape. This is only a theory so be careful not to use anything too gluey.
I use CJ Ward of Burton on Trent who do powder coatings and low temperature stove enamels. The latter look better in metallics but are more likely to chip.
