If you silicone a piece of glass over the holes it is the fay seal not the fillet that is of concern. Fay is between the two surfaces and fillet is around the edge. I work for a large aircraft manufacturer in the Pacific North West and per our spec if you apply a 0.02in ish ( and I mean ish) thick layer of adhesive and get squeeze out (this is very important) all the way around (absolutely important) then you are good. Use clear glass and clear silicone so that you can see if there are any air bubbles trapped. After fay sealing, you will want to fillet the edges. Where the patch is against the other pane ensure there is adequate silicone to fill the gap and then fillet over that as well. I have 2 glass patches in my 220 gallon tank and this is how I installed them.
