Silicone is a compound that contains silicon. Given the small amount of silicon reported (13PPM) I think it would be very difficult to prove or disprove, by visual inspection, that the gaskets were the source of the silicon. Could have been some manufacturing residue on the new gaskets. Given that a new air filter was also installed when the valve cover gaskets were installed, and the sample was taken during winter operations, I'm more inclined to believe that the gaskets were the contributing factor. Cause and effect or coincidence? Your call.
Dust is a compound that contains silicon -- almost 50% by mass. Siloxane (silicone ) contains ~28% Si.
So what's the more likely source of Si in the oil? The constant ingestion of silica (dust, dirt), combustion, and deposition into the oil through the combustion chamber OR the thimble-full of oil that touches the < 1mm * 482mm * 4 of exposed silicone gasket material inside the rocker arm/cylinder head?
Possible causes - some or all:
1. an air leak between the filter and cylinder heads
2. hole(s) in the filter media
3. particulate size smaller than what the filter can catch...
...and for what it's worth, I'm running with silicone gasket seals, and my Si report is very low -- 4.4ppm...
Personally, I'd be looking for air leaks in/around the air filter, or induction leaks -- have you noticed a wonky EGT reading? popping when you close the throttle?
P.S.
One additional thing that I forgot to mention, Siloxane won't break down until it exceeds +230°C (+450°F) for a number of hours. So, unless your cylinder heads in the gasket area are at this temperature or higher, the gasket material isn't the source of Si in your oil analysis.
This is why some cookware, oven mitts, cookie sheets, etc. are made from Siloxane.