Here's a "maybe" solution that might make things a little better - even though I'l offer a personal opinion that you're really sweating the small stuff by worrying about the step change in bootstripe (or bottom paint) change in coating thickness.  But anyway...

You might very carefully feather-sand the current sharp edge, without touching the "low" side hardly at all, and if you do, only within 1/16th inch of the line.  Just a fingertip and 320 grit or something like that.  Then run a new line of good quality edging-type tape just 1/16th or 1/8th inch or so away from the existing line.  Then repaint along the edge. (Hopefully you don't have to paint the whole bottom to make adding another coat of paint look OK.  But here is the "trick" - if you carefully pull the tape while the paint is still quite wet, and can do so without creating any "strings" of paint that wreck the clean edge, the paint along the edge will then naturally flow/thin out such that you don't have the sharp step left at the edge, as is the case when you pull tape from an edge that has already dried.

Maybe you do some testing prior to trying the real thing.  Anyway, pulling tape, if possible, while the paint is still quite wet always helps to prevent the sharp-stepped edge you're concerned about.

 Thanks Bubblehead (never said that before).  Sounds like this is normal and so probably fine to leave as is. This is my first boat paint and it was seeming to me the uneveness might present a problem by making it easy for something to catch on the lip of the raised paint and peel paint back. 

Just didn't know if was supposed to be flush for good reason or if that was just being picky.

Next time I'll try peeling the tape when paint still wet and see if that helps.

Appreciate it!