I don't worry about it because I am always merging for the purposes of re-splitting into chapters and just "assume" they will be small enough when done. Besides, not sure a Kindle has the page size problem anyway, isn't it only certain devices that do?
What I *do* worry about is double checking that Sigil hasn't thrown away the text instead of merging it. I have had that happen a couple of times - once after about an hour of s&r/editing operations where I hadn't clicked save first
(I am not running the latest Sigil, and yes this is heading OT in the wrong forum, sorry).