Covenant isn't just tracking behind Prometheus overall. It has made less every single day of release. It isn't going to catch up, not according to the predictions of experts. If you look at the numbers more closely, you will see there is no mathematical possibility of Covenant out grossing Prometheus.
Also, Ridley Scott proudly reuses sets all the time. Katherine Waters on wears Matt Damon's Martian wig during reshoots. From trailers I could see pieces of the sets from Martian in Covenant. I bet he used stuff from Exodus, as well. The set for Kingdom of Heaven was such a masterpiece of reusability that people still use it. Just saw it in Good Kill.