Probably a lot of ways to skin that cat. I'd wrap a tongue depressor in 220~400 sandpaper and use the edge to sand along the joint. That should leave a roughened strip about 1/16 wide on the plexiglass, with a similar strip on the edge of the fiberglass.
Or...don't do anything now. At some point you'll need to start working toward a nice clean edge where the finish paint laps onto the plexiglass:
It's pretty much done with fineline tape and making tape:
However, seems to me that I've seen some canopies where the builder buried the paint edge under a filet of material,
after painting. The visual result is a narrow accent stripe along the plexiglass edge, like the rubber seals around an automotive window. To do it, I'd try running fineline tape where I wish to define both edges of the filet, wipe it in so the edges are only tape-thick, then pull the tape as soon as I think it won't be too gooey.