I have been very happy with my silicone sealed portights. 1/2" plexi with a RTV (room tempurature vulcanizing what ever that tells you) black gasket silicone. The main thing with them though is that the silicone acts as a gasket not an adhesive, the windows are screwed in with stainless screws and I let the silicone cure before tightening the windows down. It stays soft even in the sun, most other products like sikaflex or 5200 will harden and eventually the window after some unpreventable twisting will leak, but the silicone is still as soft and rubbery as the day it first cured.
Silicone can function as a compressive gasket. It does not function well as a sealant.
The problem comes in where it is allowed to come in contact with wood or fiberglass. The silicone oil
seeps into the gellcoat, and even into the fiberglass it's self.
Paint will not stick to it, neither will epoxy. Some make the error of thinking that automotive solutions will work for fiberglass... in automotive prep work, silicone is a big problem because of silicone based waxes. The difference there is that the silicone is MUCH easier to remove from the metal surface then it is from fiberglass.
Many have suffered as I have with this problem... I have had to actually chisel out sections of fiberglass after experiencing epoxy and paint failures where someone had slathered silicone sealant onto a surface to 'stop a leak'.