That particular example isn't really an oddity; it's a pattern. The "-chen" used in "Mädchen" is a suffix/diminutive and it nearly always transforms the original word to the neuter gender. The original word modified in this particular case has fallen out of common use AFAIK, so it stands out as unusual if you aren't looking more broadly.

Sure. The point is that in languages with grammatical gender, the grammatical gender doesn't necessarily match the semantic gender anyway. (e.g. -chen)