Stratification offers no benefit to the A players; all of the benefit is to B and C players (and then only when they do well compared to the other B and C players but not so well compared to the A players). I see no problem with this, either mathematically or applying common sense.
The problem is this. Suppose there is an A/x section, and B/C section, and a Senior section. The awards for the A players are based on the total number of tables. In other words, the A players are given credit for beating the B/C players and the Seniors, even though they are not competing against those players.
To choose an extreme example, (Wednesday of the 2004 Monterrey Regional), there were 28 pairs in the A section, 36 pairs in the B section, and 112 pairs in the Senior Section. The players in the A section were awarded as if they had had their placings in a 176 pair field.
In another tournament, there was an Open Pairs (with 95 pairs) and a Senior Swiss Team (with 74 teams). The players in the Open Pairs got credit for beating all of the players in the Senior teams. So the first place pair won 31.24 masterpoints, which is the formula award for being first place in an Open Pairs with 246 pairs. (These numbers do not exactly add up correctly, but remember than 74 teams is equal to 148 pairs.)
Therefore, stratiflighting, as opposed to stratifying, is all advantage to A players. There is a disadvantage to B and C players, compared to stratifying.
Stratiflighting maximizes masterpoint awards (and hence masterpoints per person). When a field is just stratfied, a B or C player might take an A award. When the field is stratiflilghted, this doesn't happen -- all of the A awards are given out (to A players), and then all of the B/C awards are given out.
Reasonably, the B players should pay for the opportunity to win the B award, and that payment should be forfeiting the right to win the A award. Mathematically, this is completely defensible. Essentially, the B players are entering a tournament of other B players. This tournament is being held inside a larger tournament, but the scoring does not consider the A players. Within this smaller tournament, the awards are based on the number of tables and it is quite fairly only a percentage (80%) of the A awards for the same number of tables.
Alas, there is no obvious formula for computing what the A players should receive. I think they should receive credit for beating only a proportion of the B/C and Seniors. This proportion should probably be fairly high -- it seems that when a field is stratified, most of the A awards usually go to A players.
However, with the current formulas, there is not as much benefit as there should be for increasing field size. So at the extremes, the A players receive the benefit for beating a lot of players that they are not really beating, but the reward for beating those players is not as large as it should be (if they had really competed against those players and won).
This changes if my award system is adopted. Now the presumably unfair advantage for the A players would be exacerbated.
The second ameliorating factor is that anyone can join the A flight. They are the X portion of that flight. They actually compete against themselves, in addition to the possibility of winning an A award.
Finally, I suspect that B/C do not enjoy playing against elite players. Yes, it is a thrill to play against someone you have read about. But most of the elite players are not famous. No, it is not fun to be beat up by elite players. A score of 45% in the A field might be much better than a score of 55% in the B field, but it doesn't necessarily feel that way. And no, it is no fun to play against players who use bidding conventions you don't understand and, worse, who use strange conventions on defense.
The Senior section is slightly different. The idea behind it, if I understand correctly, is to allow A players who aren't as good to compete away from the experts.