Maybe they want to establish that the Supergirl setting is not in the current DCEU and never will be since, in the current DCEU, Supergirl doesn't exist yet let alone show up on Earth before Superman. It may be they want to subtly unravel the current DCEU and rewrite it without admitting that's what they are doing with a blatant restart.
Then again, they seem to be forging ahead with DCEU stuff so maybe, with Cavill out and MoS and BvS being regarded as a big mistake in direction, they just want vast distance between Supergirl and Superman and, yes, an excuse why Superman wouldn't be there.
Then again, if they forge ahead with anything like another Justice League movie, I think they'll have major problems without Superman just as they had major problems even with him.
Let's face it. In terms of popular appeal, they so totally messed themselves up with their foundations for the DCEU that they are just treading water and trying everything to see what works.