@roger64: Yeah, cr3.ini is NOT shipped with KOReader, it's built at runtime the first time a CRe-handled document is opened.
But your detailed recap of what you did was perfect, and answered my question [you indeed got a 'new' cr3.ini, whith the changes I linked to in the KOReader thread]

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So, without further ado: it's probably because you're used to the previous font rendering settings, which discarded font hinting completely. I tweaked those (because they were fairly insane), and we now default to using FreeType's autohinter, which tends to be very generous when bolding fonts (much like Apple's rendering, which roughly does the same thing: discard the font hinting, and do it heuristically instead).
So, you have two choices if this bothers you this much:
• Go back to the previous settings: set font.hinting.mode to 0 in data/cr3.ini
• Enable bytecode hinting (à la Windows, which is what the Kindle (and possibly Kobo) stock readers do: set font.hinting.mode to 1 in data/cr3.ini
(FYI: KOReader's UI probably defaults to using bytecode hinting, too, IIRC, but every other document-handler doesn't handle hinting (which is fairly stupid, if you ask me... It's much less annoying because those devices are relatively high DPI, but, still...)