I work in a body shop for a pretty good number of years and built cars on the side for shows. And this doesn't mean I know everything or even pretend too.
Powder coat will not stick to the seal sealer for long if at all. If you use silicon it will fish eye.
If these were my fenders and I wanted them to last I would find a good body shop. Have them use a high build epoxy zinc primer water sand them seam seal all the areas that need it. Then have them painted to the colour of your choice, and just because I know from my past experience I would bed line the underside.
This would take care of just about everything.
(If you find a good body shop they will be able to seal top of the fender so that it looks mint. If it looks anything less your probably at the wrong shop).
Again this is just my own personal opinion and what I have seen in the past. I would skip the powder coating altogether. That said this likely would not be cheap either.
Hope this helps.