United beating Viktoria Plzen makes more sense to me than beating Man City in the Manchester derby after that. Viktoria Plzen and United are level on points now, but I don't see United falling behind in the game. They will be the favorites.
The points will be crucial for them in their bid to progress further in the Europa League. In the Premier League, I think the competition will be much tighter. Amorim still has a lot of work to do to see United perform well.
Comparing the 2 clubs that Manchester United will face, it is clear that their match in the Europa League will be easier than facing Manchester City in the Premier League which will take place this week. I agree with you that this makes more sense.
However, I cannot rule out their chances of winning when facing Manchester City, because Manchester City is also currently in a bad state, so that will benefit Manchester United. But it still depends on how Manchester United performs in that match, because if they play worse than Manchester City, then they will also lose.