An organised squadron could be certain, though - require that people log their activity to Inara, or EDSM, or just send Journals to the squadron leader, and assume they're performing poorly and kick them if they refuse. The effort required to convincingly fake the journals would be more than the effort required just to do the hauling/shooting/whatever.
Basing it on the squadron's maximum size during the season would be harder to actively exploit, sure. But it does encourage kicking out basically everyone but your top performers near the end of each season, to get your size down before the start of the next season. I don't see why actively encouraging squadrons to be smaller is a good objective.
The other problem is that it makes the in-season leaderboards basically meaningless. At the moment I can see who is in first place, who is in second, how much effort it would take to catch them. If squadron sizes mean that points are then retroactively rebalanced for the final scores, it might be very difficult to tell who's ahead right until the end. If you look at lot of the leaderboards, competition for the trophy places boosts the performance of all the squadrons in contesting distance: if no-one can tell who that might be until day 58 or so, then a lot of the potential excitement is gone, replaced by a lot of spreadsheeting about "can we afford to keep Bob?"
I still fundamentally don't get the objective, though. Let's say we each have a squadron. In season 4, we both have 10 players in our squadron, and your squadron beats mine into 1st place by 1100 points to 1000 on a particular leaderboard. In season 5, you recruit 10 extra players, who don't do anything towards that leaderboard, whereas my squadron keeps a static membership. We both put in the same performances in season 5, so again, your squadron scores 1100 points and my squadron - having done absolutely nothing differently this season - scores 1000 points. But, because you recruited some extra deadweight, my squadron now wins. We didn't do anything to earn that win. We didn't recruit new talent. We didn't train our existing pilots better. We didn't find a new way to score points quickly. We didn't work harder. And your pilots didn't do anything less than before - it was still the same people beating us on points in the same way. But now we win? Because you were one squadron of 20 rather than two squadrons of 10? I don't get how that's a desirable outcome, or how discouraging you from taking on those other 10 is desirable either.