First, silicone is a bear to remove from portlights. You might try a brass brush wheel on a bench grinder along with many different types of nasty solvent.
Second, count me as one who actually likes butyl tape to install portlights. It's easy to remove the portlights if needed, it cleans up with mineral spirits and its non-messy to apply. I have successfully bedded 12 portlights on two boats with butyl with only one leak that appeared immediately and was easily fixed by pulling the portlight out and adding a bunch more butyi to an area that was a bit thin. The Bed-It butyl from Maine Sail is superior to all others. Loren is right, the butyl will deform the portlight frames if it is cold. Use a heat gun to soften it up (or pick a hot day), and tighten the frames down slowly over a day or two. Don't pull off the squeezed out butyl until you have done several rounds of heating and tightening (it's easier to get a clean line pulling it all off at once). Might be worth a try on one and if you don't like how it turns out it's easy to remove all traces of butyl and start over with a sealant of your choice (SikaFlex 291 gets my vote too).
Also, if you aren't happy with the rubber gasket (I ordered two different sizes from CatalinaDirect but never found one that fit the thick tempered glass in my portlights), you could use a heavy bead of Dow 795 in the frame and bed the glass directly into it. 2 years and holding on mine so far. Note that this is a fairly permanent solution. Hopefully it will last many years. Its used to install glass in aluminum channels on high rise buildings so it should be pretty good. I figure when it starts leaking I will have moved on to the next boat, or I will replace all the portlights with newer versions rather than trying to excavate all that 795. Also a $5 rubber profile caulking tool is great for getting a clean edge.
Oh and make sure if any silicone is on the cabin top, to remove it, you may need to be sand down the gelcoat a bit to give the butyl or sealant something to grab onto.
Good luck