Yeah it doesn't really matter, though the two cities that are beneficial to be friendly with are Neriak and Cabilis due to key encounters that take place in these areas (Verina Tomb and Vessel Drozlin). So if you can preserve faction in any cities those would be the two I recommend. An enchanter with no faction hits should have no problem moving through these cities with dark elf / iksar illusion. Just a matter of convenience though, not necessarily required.
Side note - though not really a city, another faction that would be worth working on is Chardok for the Prince Selrach part. Very helpful to be able to move about that very dangerous zone with no issues. Would recommend saving up some plat for the goblin skins needed for that faction.
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