I think Larian probably did it so the Backgrounds felt more substantial. If you can choose any Background with any skill, it kind of makes the Background selection irrelevant. However, as it is now, choosing Half-Orc and Soldier is just suboptimal because you lose a Proficiency (Soldier and Half-Orc both grant Intimidation). To fix it, I think you could choose a Background that has 2 Proficiencies and allow the player to change one of them either to anything (if Larian wants to leave it in the player's hands) or to a subset that matches the background somehow. I think it is easier to just let the player swap one of the Background proficiencies for anything else and easy is important when they have so many other things they are probably working on.
They could also go the route of making Background Skills into Expertise if you make a class choice that matches the Background skills. That deviates more from the 5e rules, but it certainly makes the Background selection an important one, if that is the goal. I'd personally prefer that because I think Expertise is underutilized and the way it is now, players are discouraged from making choices that seem appropriate (like Shield Dwarf + Fighter is a suboptimal choice). It also gives Wizards an avenue for getting Expertise in Arcana, which makes sense to me.
