My guess is they simply didn't really pay attention to this possibly happening, as the chances shouldn't be too high. You after all need to have the old regular commissions set to the same area you want to do quests in AND then be (un)lucky enough to get a commission that overlaps with a different quest you want to do. Like if you already did all Mondstadt quests and set your commission area to Mondstadt, there will never be an overlapping NPC. And once you did the non-repeatable quests they're out of the pool of potential overlap, too.

This overlap can also apparently be used to get achievements relating to daily commissions faster: By having a non-repeatable quest at a point where it overlaps with a commission, you block said commission from popping up - unless they removed this with the latest update ofc. This speeds up the process of cycling through the region's commissions. Link to the collection of guides regarding commission cycles (not done by me, all praise goes to the actual guide maker): https://hoyo.link/80GCFBAL?q=22AsDtWx4Uh

I know the feeling well. As someone who basically unlocks and starts the beginning of every Story Quest, its somewhat hilarious when you stumble upon them.

I remember the Unusual Hilichurl event and accidentally stumbling upon Xiao's story quest which contains weird hilichurls. Or the start of the Weinlesefest with Kaeya suddenly having a much more subdued tone when I triggered Jean's quest.

I don't really get what qualifies for "actively blocking" or not. Hu Tao has been standing in Wuwang Hill over the Oceanid fight for years now and it's never been an issue.