I've only used pre-kote once, on my first build, and although things turned out fine I wouldn't do it again, for all the reasons mentioned.  The most significant to me is/was that if you end up with more than very small defects filled by pre-kote, or areas of pre-coat of any significant thickness, you do end up with a soft foundation under your paint, more easily prone to scratches & etc.

Extra coats of Brightsides are an expensive way to go for a smooth finish - expensive material, and only able to put on in thin coats.  You also suffer the 24 hrs between coats penalty.

So, I recommend epoxy with micro-balloons.  Easy to fill even larger defects, easier to sand than epoxy (but that doesn't mean it sands really easily, just easier).  And should typically take only one coat to smooth out almost all issues, if the hull was even relatively well finished prior to the micro-balloon coat.  Don't make the mixture too thick or "dry" with micro-balloons thinking that will be better - it will not flow/self-level as well as a slighlty thinner mixture, and a too-thick mixture will tend to want to "clump" as you brush or roll or use a scraper to put it on the surface.  For some reason the mixture behaves a little differently than cellofill or wood flour mixtures with this "clumping" tendency.

As a second choice to microballoons I'd just add and sand epoxy coats until you are happy.  

Know in advance that even the SLIGHTEST surface imperfection gets highlighted and magnified by the gloss paint.  So if you know you have "micro-imperfections" as you note in your posting, it is very probably that they will be visible even after 3 coats of paint.  Even sandpaper grit swirls for grits harsher than about 150 will show in at least your first coat of paint. So if you don't see a 100% smooth "gray" surface after sanding your epoxy, know that it will show up in your paint job.  My paint jobs are always less than perfect, but good enough for me, and pass the "10 ft." test.  Just depends how concerned you are about the finish and how much time and effort you want to put into it.

Is your sander attached to a vacuum?  If not, highly recommended.

   Thanks, Bubblehead (sounds wrong to say that), I like that plan. A thin coat of microballoon filler applied with a Bondo squeegee, sand, and follow with 1 coat of unthickened epoxy sounds manageable and hopefully gets me to a 7-10ft finish.

Hopefully I can get the finish on before summer heat gets here for real. As for the vacuum, I'm pretty much hand-sanding it all.

   I'm one of the ones who won't PreKote again!  I used Flattening Agent in the dark green for my skerry and since I got tired of sanding before the surface was truly flat, I'm happy to have a semigloss as opposed to gloss finish.

I used some microballoons on the deck of my wife's Kaholo because I f'd up the puzzle joint a bit.  Keep in mind they can't fill the very small divots, and you will still have some sanding, but it really speeds things up if you have some prominent dips or drips.  And the lap does help hide some smaller issues so don't get too obsessed with the dips right under the laps.  You can sand through the epoxy and even glass easily right on those corners if not careful so go easy there.

Get a vacuum with HEPA filter on that sander!