It looks like this isn't boosting TEs enough in TE premium, and it's boosting them too uniformly.
Switching to 2 PPR for TEs (with 1 flex spot) appears to give every TE about a 1.5x boost (or slightly less) compared to 1 PPR. It should generally be more than that - last year the total TE value with 2 PPR (and 1 flex spot) was about
2.2x as much as with 1 PPR. The highest scoring TEs get the smallest boost (as a ratio) - 1.5x basically matches Kelce's boost from last year, while Hockenson was worth more like 2.6x as much with 2 PPR vs 1 PPR. But the trade value calculator is just giving them both about a 1.45x increase in value (which I switch from 1 PPR for TEs to 2), and it isn't narrowing the gap at all.
Things are different without a flex spot - in that case the calculator looks about right. TEs score about 1.35x more with 2 PPR as with 1, and it's still just the same 12 guys starting, so TEs should be worth 1.35x as much in 2 PPR with no flex spot as they are with 1 PPR and no flex spot. That is basically what the calculator does. But with a flex spot, you have more TEs starting each week, which means more guys accruing value and also a lower baseline (last starter is TE19ish rather than TE12). So TE premium matters more.
A simple-ish check you could run is to calculate the total VBD last year for each position, in each scoring system, and see if the relative values of the positions in last year's VBD roughly match their relative values in total trade value. More ambitiously, you could go back to (say) the 2000 offseason, where you know each player's future, and calculate the actual future value of every player in each format, and see if the shape of things there basically matches the shape of things in the app.