Honestly I'm also disappointed by this behavior. How about adding a Wallpaper Engine Compatibility Mode to Fences that disables all Fences features that conflict with WE? That said since 3.09 works it can't be that much that is truly incompatible.
That said, here's a tip from someone that partially studied economics and business:
Forcing customers to use your product over a competitors by using such tactics rarely ever works, if you want customers to use your product instead you have three options:
1: Make a better product
2: Outprice the competition
3: Remove the competition
2 and 3 aren't really possible with Wallpaper Engine so I would say either do 1 or leave customers in peace.