Though I generally favour the 'Aylieds are absorbed stance' not least because it supports the Mythic Dawn are hokerrs thing i also considered longevity.
Given mer live 500 - 1,000yrs even though they can breed (when they do) at a fairly young age, so 3,000yrs could cover only 3 - 6 lifetimes. Long enough that many living Mer could be talking of their grandfather/mother or great grandfather/mother the famous Ayleid so-and-so. and I suspect that mer are more conscious of their heritage - after all their parents, grandparents, greatgrandparents etc are around long after they reach maturity barring accidents.
So there are likely many genetically distinct/obvious Ayleid types in the population even if the Ayleids as an organised culture decided to call it a day. I truly doubt they ALL went out of their way to breed into the local population - though love is where you find it.
Where did you get that from? Even Altmer only have a life span of a few hundred years. Most elves don't even reach a hundred and fifty.
Only very wealthy elves (and talented magicians, obviously) reach such a high age as 1000 and above, since only they have access to the kind of good medication and healers needed, combined with that they don't have to work, or risk their lives in any other way.
The life span for Wild Elves would probably be even less than for a Dunmer, since they're essentially live in a harsh hunter-gatherer society nowadays, and have for quite some time. If the ogre or bear don't get them, they probably succumb to disease or infection before they reach their full "age capacity".