In Prometheus, Elizabeth Shaw and Charlie Holloway are scientific partners who are also in a relationship before the events of the movie. They discover the location of LV-223 and get the support from Weyland to fund a scientific trip. It is entirely coincidental that they are in a relationship, though of course that fact is used later in the plot. They are a couple on the ship because they are responsible for the expedition.
The situation in Alien Covenant is entirely different. This is a colonization ship, a deliberate, one-way trip to settle on another planet. It is clearly deliberate that the ship is (entirely?) crewed by couples who are likely to want to settle and raise families in their destination.
I don't think you can extrapolate the second example to say it is 'encouraged officially'. Its clearly encouraged, possibly a requirement for the people funding a colonization of another planet, but why would it be a general requirement? The trip in Prometheus and the later Nostromo isn't one-way and is largely crewed by single people.