I agree that silicone is not a good sealant to use on an engine. Because the squeeze out will break off and clog oil galleries. But I notice it is the sealer of recommendation these days on my truck differential. I used it there because like the primary on a Commando, it won't really hurt anything if some breaks loose inside. However, I read a tip here in a long ago thread that I have used on my primary and think it is worth repeating.
Because of the large area of the sealing surface on a primary case, being fastened with a single bolt at the center, it is a good one to worry about whether the faces are true. But if you pull out the gasket (O-ring) and put a small bead of silicone gasket maker in the bottom of the groove, you can then put in the O-ring, replace the outer case and tension it but do not tighten it down until after the silcone kicks off. This process allows the O-ring to form to the outer case mating face and match any irregularities in it. After the silicone kicks, you can remove the outer case, clean off any areas that may need it, and then put it on with enough tension to compress the O-ring.
Following this, made a big difference in the leakage, or lack of it on my primary. I don't know who the tip originated from, but am thankful they posted it.