Ok so here's an update as per the suggestion of @Andrew James
I filtered my results for players >=130PA in loaded leagues only (~5k vs ~8k before) and here it is
Loaded league players do develop better, but I'd hesistate to call it well, as they're still on average 6.6 points behind at 25 vs 12.6 with non-loaded. The worst is actually -10.4 at 21, whereas with non-loaded league players it was -13.94 at 26
So I guess if you want to play despite this at least load leagues as opposed to loading players though the custom database setup. It reduces the impact of the problem
Players transferring in from unloaded leagues might still be affecting this but if you're running a large DB this is likely to happen to some extent anyway. Reducing the DB size and loading more leagues instead might make the issue even smaller. Just don't expect as many cool super exotic wonderkids if you don't load the league I guess
Loaded leagues only spreadsheet