I think it's on purpose because Andor can't have a real anti-fascist, anti-empire message if Darth Vader is present. In the dynamics of real empire, Vader should be some kind of manager/general like Krenic. He can't be a 6'-4" cyborg who is the best at being a pilot and the strongest magic space warlock to ever exist. The foundational narrative of Star Wars is about how empires are created by bad people who are indoctrinated by magic space warlocks. This message was driven so far deep in the lore that literal space genes cause people to be almost deterministically evil or good. You can't be materially anti-empire when the empire is actually magic. Being a revolutionary against empire means something and it's not waiting for the prophecy of a good guy with magic space genes to save us all.
The best thing Andor can do is forget the Skywalker bullshit, pretend it doesn't exist, and flesh out the Empire as being founded in material exploitation. That is something they have been doing so far. If Andor has to go find a magic Jedi mcguffin or protect the royal space gene bloodline, it's cooked. Luckily we know how this ends so they don't have much room for that bullshit.