Silicone should be fine there. I've never sealed mine and I just leave the drain plug out of the front. I've never had any problems with it. If it's glued up I figure if water gets in then it will be harder for it to get back out. Even worse if the crank seal or welch plugs leak.
I've never glued any customers ones either and never had any complaints.
If the gearbox is sealed properly with the right stuff and the breathers are working water shouldn't get in anyway. The factory gearbox sealant is pretty damn good and will last a lifetime unless the box has been pulled apart before.
As for the bellhousing and clutch, The cover/sandwich plate between the motor and bellhousing needs to be sealed both sides with a high temp RTV silicone type gasket sealant, around the starter motor too. But best done when it's still separated and going back together.
Another spot is the rubber boot around the clutch fork, that has to be sealed exceptionally well.
I always leave the plug in the bottom of the bell housing as well.
Done all the above when I put another box and transfer in and I've never had water get in my bellhousing or gearbox.