Well the if the competition at Strade and UAE was not great the same could be said about Omloop and E3... plus Pogačar was the strongest rider in Flanders still getting 4th and 5th at MSR.Spring
For Pogacar UAE Tour and Strade weren't that impressive when you take the competition into account. Tirreno was though, he was amazing there.
In case of WVA, he was basically the best in every cobbled race he started in. He won Omloop, and E3. Single handedly got the Paris-Nice victory for Roglic and finished it off with a 2nd place in Roubaix and 3rd place in LBL.
How did WVA not have a better Tour than Pogacar? Not only did he win the green jersey, the first stage he won was amazing, and he outclassed the whole peloton with that 10km solo towards the finish. And after he basically won the green jersey, he was the best uphill help for Vingegaard, and for a moment made Pogacar crack on the Hautacam. Knowing how much WVA weighs, that's pretty impressive.
Being runner-up in the Tour > Green Jersey. If Pogačar hadn't done anything else in the Tour I could agree with you given the amazing Tour that Van Aert did but he also own three stages, wore yellow and attacked left and right after he lost it.
If all that I said isn't enough to decide between Pogačar and Van Aert, the fact that Pogačar won a monument and Van Aert didn't (once again) should be enough to put the Slovenian ahead...