The deck of your Destroyer will be approx 20mm thick. Find the thickest screws possible and get a few of these. For your main fixing screws use one size thinner. This gives you the opportunity to fit a thicker screw should you strip a thread while tightening. Plywood isn't always as homogeneous as one might like.
I have no problem with you using sikaflex but I wouldn't use it.
What no one has mentioned and is essential if you want a good job done, is to ensure the area you are jointing to is degreased, the seat base is degreased and also the self tappers are degreased. I put them into a tin of thinners and agitate it with a wee paint brush then tip them out onto a rag or bunch of paper towel. Make sure your drill isn't greasy or oily and, because you're screwing into plywood, your pilot drill needs to be the same size as, or very slightly smaller than, the root diameter of the self tapper.
I don't know what your seat flange is like but you need to drive the screws in nice and square to the deck. I'm presuming you've got holes in your set flange. To ensure accuracy, place the seat in position dry and, using the same drill size as the flange holes, drill into the deck at one corner just enough to make a depression. Move the seat and pilot drill this hole. Put the seat back and fit a screw but don't tighten it enough to stress the thread it makes. Align your seat and do the same process in the diagonally opposite corner. Now you can drill the depressions through all the other flange holes and be sure they are well aligned. Remove the seat, pilot drill the holes, brush away all the swarf, degrease again to be sure, skoosh sealer down every hole, apply the sealer to the flange and screws and fit them being careful not to overtighten them.
For sikaflex, Richard's recommendation for masking around the area is very good. Sikaflex is blacker than black....provided you buy black stuff, of course.
I personally think self tappers, if done well into good material, are seriously strong.