But indeed, the x and the ⃝ are from different fonts, so this isn't
surprising.

We have a number of open bug reports in this area.  At least 44784,
23292, 17739, which may or may not be the same underlying problem.
(Probably different issues, really.)

I haven't looked at the machinery here at all -- is there a fundamental
reason why Emacs can't combine glyphs from different fonts?

-- 
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   bloggy blog: http://lars.ingebrigtsen.no