Bearing in mind that it's only my opinion, fella, but I reckon that it's better purely for the reason that you mentioned of 2 top level guys taking points off each other.
I think it's only really best for the factory when you have a phenom like Marc in the number 1 seat with all point gaining focused towards the championship.
The brass tacks is that it's just a feeling that I have. I don't have empirical data to back it up and I've made a pig's ear of articulating myself.
Realise it is your thoughts and all good, I just come from a different school.
For mine, if we use Marquez as a guide, he is that kind of talent where you do not need a #1 or #2 (officially) within a team as Marquez is such a rare talent that you will not have an equal in the team based purely on chances of it happening.
The closest we have had in the last 20 or so years has been the Yamaha garage of Lorenzo and Rossi, and if we are fair neither of those two cost the other the title and likely drove the other to higher standards.
For my way of it, to have a #1 and #2 is already displaying a heirachy which does not bode well for team harmony nor recovery should #1 not work out, be injured etc.
Of course there are exceptions but all of the exceptions I can think of are older riders who have gone to a team where there is already that extreme rarity of talent (Edward to Rossi for example).
I understand where you are coming from and would say that in some classes it would be possible or make sense, but when you get to the top of the game the issue is the individual's ego which rules so much of what they do, why and when.
To me, the cream will always rise to the top no matter who their team mate may be.
I should add that where a younger guy is a good choice for a #2 is for those teams that may be struggling financially as sometimes that younger guy will take a small paycheck for the opportunity to prove himself, but again you then have him determined to beat that team #1.