Especially for square section, I use a little "Shoe Goo" or their marine variation since it can be gotten off after a decade or so if the cloth wears out.
I have the boot inverted pointed up a bit higher than it will actually go - pays to practice and mark before any gooing. Pick up a bit of the edge against the mast and squeeze a bead of goo all the way around. Then start frapping from above (on the mast) the goo bead down so your squeeze out will be inside. Once that's completed, fold the bood down and into place to frap around the collar. The goo bead will keep the water from running in on the flats. Even on a round mast it's nice because with the boot folded down you have a cloth ring that tends to hold rain water against the mast and let it dribble unless sealed. Once running down the outside, it will be fine. Modern fabrics might be treated with silicon but natural cotton will swell.
G'luck
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