You're right in practice, but for clarity it's not because it's after the subject, it's just that it's the noun/verb object of a short form verb (a verb with a stem and ending). So in formal language where pronouns are often dropped, the mutation still holds e.g. Ga i ofyn? as A gaf (i) ofyn?.
We know Welsh borrowed the word from Middle English "questioun" (which in turn borrowed it from Anglo-Norman from Old French from Latin) but it's impossible to say whether it was borrowed as a written or spoken word first. Over time both Welsh and English spelling systems have been standardised and so they each write the word in their own way.
Interesting that the Middle English spellings "questioun, questiun" seem to indicate that the final vowel was an /u/ kind of sound. This has changed in Modern English but has been kept in Welsh. You often see that.