Hi Greg,
I replaced the windows on Tales a few years ago. Frames too as they were corroded.
Used the same system as original because bolt on, for Tales, would not have been a good look.
The cabin and deck surfaces are not true to each other (not in a straight line) and with enough filler to give flexibility the windows would have stood out 10mm or more.
The biggest problem with windows is that they change dimension at a different rate to the fibreglass in heat/cold/wet/dry and any adhesive sealant (if not really thick) eventually fails. It could take years though.
The length of the Mk III window makes it worse. Addiditionally, the original had a light vertical brace included on the inside trim. It doesen't look like it does much but if you leave it off, the cabin top and deck below flex quite a bit when walked on.
The original type of windows on the Mk III used the rubber section as a seal. The silicon or whatever is used only as a spacer to centalize the plexiglass and does not go between the frame and glass, just around the outside of the glass.
I made up a brace which also doubles as a hand hold and reinforced the structure between the headliner and deck locally.
Regarding drilling windows, some people use a blunt drill but tradesmen use a drill sharpened for plastic. The rake angle must be reduced from positive to zero. This will stop the drill pulling into the material and making cracks when it breaks through. Additionally the edges of the hole should be lightly releived with a multi flute countersink (not a drill bit).
Lexan is very attractive as it has the reputation of being 'bullet proof' however this mostly relates to bending. In tension it is not much stronger than anything else so if it has holes drilled in it and is held securely, side loads (breaking wave) will cause tension force and tend to break it at the holes. Extra thick windows with oversize holes and thick sealant would go a long way to help here.
The windows on Tales are ok and they don't leak but they fret a bit with the movement and I feel that 10 or 15 years will be the limit. Like a lot of other boat stuff I guess.
Cheers,
Tom