1- Without looking, the plastic moulding probably snaps into the frame,
not around the perimeter of the glass. I'd still leave a little wiggle
room, though.
2- Use
something that isn't too difficult to clean off for the next guy, like
latex. It'll be on the inside, not too exposed to the weather.

3- The moulding holds the pane, the
caulking keeps it from rattling during thunderstorms, and seals air
leaks. Tom