It is a contradiction, and I don't know the history of why the USTA came to this decision. What occurs to me is that the USTA doesn't publish exact ratings (like that I'm a 4.26 and my opponent is a 4.33) so it is still subjective who is stronger. I'm sure the USTA doesn't want a flood of complaints that if the lines are supposed to be strength based, that some time didn't play the teams in that order, and the USTA wasn't want to be arbiter.
What we can take is that in plus leagues, the strongest players are on line 1, so that seems to define the intention, and most leagues/captains abide by that.
That makes sense.
And actually strongest *is* subjective within a level even if there were exact ratings, since there are so many variables involved - current form, injury situation, singles vs dubs, stylistic match-up against opponent, how a pair complement each other in dubs, etc.
Even in plus leagues a plus rated player is not necessarily stronger because of some of the same reasons - as a 4.5 singles player I've beaten several 5.0s who are more dubs players but were put in the singles spot (this is back when there were two 5.0s allowed in the lineup).
But the plus players will most often be stronger, so makes sense to have them match up against each other where possible.
OP was asking about combo? That's going to be even more of a crapshoot because having players of different levels on the court changes the dynamic as well. E.g. do you play orthodox shot selection or do you target the weaker player? And how will the pairs adjust? Etc.
EDIT: Thinking about it, it would make sense for USTA to mandate that anyone playing up should be on line 3, just like they require plus players to be on line 1. Why don't they do that?