I think filling the gap is useful, not essential. Just my 2c.
I did it because, honestly, it was easy to do with the window out, and seemed the right thing - no leaks between the cabintop and liner. But it was probably "belt and braces" as we say in the UK. But needed? Probably not.
Good tip about the Goo Gone...
And I also use butyl tape as my preferred bedding compound. For me, the most difficult parts of the job were removing all the old silicone (which a PO squeezed in to stop a leak) and getting the glass-with-gasket into the Al frame without (a) over-stretching the gasket, and (b) getting sealant everywhere! It certainly was a tight fit, I ended up using clamps to gently squeeze the whole thing together...and still got sealant everywhere.
Next stop will be replacing the four plastic opening portholes forward. I replaced the hinged "windows" a few years back, but the hinges on the frames are beginning to fail. It's only a matter of time, and I would not want them to fail when I am out there in 25kn+ and getting a salty soaking... :-)