Definitely not opposed to auto completing them, but tbh, with the exception possibly of void, you shouldn't really ever be running out of champs you want to max. Yeah you're short on resources, that's fair, but you should eventually be needing to max out more, so you'll eventually just "naturally" complete those.

If you are at this point of the progress missions, you should have enough champs that are worth 6 stars. Maybe you post a pic of your roster and we can give some advice.

at this point in the missions at least arbiter is pretty much done, and you can take your time if you want. You should have enough champs that would be worth leveling at that point either way. I agree though and was dissapointed myself when I got to this point and realized that they were not auto completed even though I had done each of these missions multiple times at that point lol.

I don't think this is huge issue, over 6 months you will be taking dozens of champs to 6 star across all the affinities. 

Is it awkward because you have to do them in a certain order, perhaps, but everyone before now managed to do it that way. Some times you just need to plan in advance of the missions coming up. 

Like Skadi said, if you want advise on which to go with drop a screenshot of your champs and maybe we can help.