According to river name specialists, many early Welsh river names come from personal names. Alun may be one; I don't have a copy of 'Enwau Afonydd a Nentydd' to hand, but that's probably the best place to look it up.
Why influenced (possibly)? Because names tend towards similar spellings elsewhere, and names are easily confused. Many modern Welsh parents have chosen place names as given names for their children, and some may be giving the name Alun through confusion with the river name, not realising that Alun is a well-established Welsh form of Alan.
Not relevant - because early sound changes are fairly predictable, and u (ih) to a (ah) has no parallels (that I know of) in other Welsh and Breton names i.e. there are no other native Breton names recorded in the Middle Ages with an a in them, for which there are recorded native Welsh equivalents with an u (ih) in them.