The only purpose for the small bolts in the main cap is to hold the bottom of the timing cover on. They have nothing whatsoever to do with the main bearing fit or strength. Getting to those two bolts from the front side was VERY difficult on some engines due to the position of the front motor mount. Putting them through from inside the oil pan was simply a timesaver when the front main bearing cap needed to be removed. Good engineering, really!
Silicone sealer has a habit of getting into places it doesn't belong, like the oil pump pickup strainer, the oil pump relief valve, crankshaft oil passages, etc. if it squeezes out into the inside of the pan. If you absolutely insist on using a sealer on the pan gasket, get a can of Permatex Super 300 brush-on liquid sealer. It's a lot less likely to get into places it doesn't need to be. Huge gobs of sealer are not a substitute for straight sheet metal and clean, properly tightened parts.
Jerry
