When I did my bulkheads I did a thin smear of silicone but probably not needed. Also silicone, if the nut is overtightened, can easily cause the gasket to be pushed out.
Two drains, YES!!!. Search for Herbie, about the quietest drain system out there, better than a Durso etc.
For overflow boxes, can't say I've ever seen rubber (always siliconed or if acrylic, bonded). It does need to be sealed though.