No adverse effect, but I'd be really surprised if it actually changed anything. The font-packages-as-update way is more likely the best way to workaround this.
As for the why, you aren't necessarily the only one, some other people have had weird issues like that (Pushka, daffy4u), and that was even *before* the full hack, but with the reader.pref & alt family tweak. So, supposedly, something is way more fragile than before regarding the framework handling of font files

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EDIT: Just switched back to my usual fonts with an update pkg, still no issues.