Hi Bill, here is my take on it.

Ideally, you should be blasting the cases with a medium such as coconut or walnut shells, or even maybe vapour blasting.

I still use a very fine glass bead, but I also turn the pressure way down.

You should not be blasting anyways near hard enough to need to mask off mating surfaces.

The main issue with glass beads or sand is that fine particles can, and will, embed themselves in the aluminum, and then get lightly peened in by the process. On motor start up the heat from the engine will then likely open up these pores and release nice grinding material into your freshly built motor. 

Whatever you do, clean rigorously afterwards with nice hot soapy water.

Glyptol fine if you wish, altho the danger is that after a while it may start peeling and leave chunks of paint in your oil. Not as terminal on a total loss bike as recirculating oil. It may prevent a little oil seepage thru porous cases but generally they are not that bad.

Carefully flat file mating surfaces to remove any burrs or flatten any dings. Don't take off much material.