Two things:
You don't want to go with a thick coat first. You want consistent thin coats that build up to 60-80 mil. 60 is about as thick as a dime or 1.25 mm and 80 is about the thickness of two credit cards (recommended by Scott at USI).
You do NOT want to apply silicone to Pond Coat. Apply the silicone first then when it is cured apply the Pond Coat over it. While Pond Coat does not bond well to silicone, you can bridge over it. Meaning that you can have it go from the wood to the glass or acrylic with cured silicone between the wood and glass/acrylic. It sticks really well to either side of the silicone.
Cured silicone will NOT break down Pond Coat over time. Cured silicone is inert. It is uncured silicone that WILL break down Pond Coat. Uncured silicone releases acetic acid (that vinegar smell) as it cures. The acetic acid is what eats at the Pond Coat.
Also, Pond Coat does NOT breakdown when submerged in water.
Just FYI, I'm looking into becoming a distributor for Permadri products.