Some transactions are unwound. Unwinding less transactions by being able to segregate transactions in the attacked fork and add to the non-attacked fork those which are not downstream from a double-spend or stolen coinbase afaics doesn't decrease fungibility? Rather it aids a potential political consensus to choose the non-attacked fork.
It does because you are imposing traceability, and with traceability comes the threat of blacklists or whitelists.
Also with the resolution of any double spend comes the judgement of which is the "correct" spend.
Monero coinbases can't be spent or used used as mixes until they are unlocked (rather short now IMO, but will probably change that) so unless the fork is prolonged, and you are on it for a prolonged period of time, none of your spends will be mixed with coinbases nor with anything downstream of coinbases. You also can't mix with an output you can't see, so the threat of chain replacement doesn't affect you as an innocent third party. Once the chain replacement is noticed, most likely exchanges (at least the well-run ones) go frozen rather quickly, and again few if any transactions will be affected.
With any coin you can certainly be downstream of a double spend with no real recourse. Lets say someone double spends to an exchange, and then you withdraw. You may very well get the double spent coins. What happens with a transparent or non-transaparent blockchain is that your withdraw from the exchange is unwound (when the other fork prevails) and the exchange is likely out a lot of coins and could go bankrupt. If not then they just reissue the withdraw transaction to you with some other coins.