Way back in 02, when the fender extenders were just getting popular....
I did some measurements and a simple model of the front fork geometry
on a cad system.
As the front fork compresses the clearance between the front wheel and the lower cowling decreases.
At full compression, the lower edge of the front fender is above the cowl
and the clearance is to the front tire surface instead of the fender surface.
Now, with a fender extender on, when the forks compress, instead of having a clearance to the tire surface, you only have clearance to the new fender extension. So there is a lot less clearance with a fender extender, when the forks are compressed.
Now, you have to add in another dynamic.
When you clamp on the brakes, even with anti-dive, there is some fork compression...
and if the front tire hits a good dip or bump at that time, it adds even more compression...
Now, add in the effects of a half ton of bike trying to push itself over the heavy braking front tire.
The fork tubes flex rearward a significant amount as they react to all the weight pushing against them.
The original configuration, without a fender extender, allows for the front fender to be above (and clear of) the cowling, under heavy compression and braking. When there is a fender extender, there is a range of motion in which that fender extender doesn't clear under compression, and it can contact the lower cowling when the forks flex backwards under braking.
One danger was if the lower edge of a rigid extension was not kept close to the tire.... it could jam on the cowling as the forks started to decompress.
You'll notice all the available versions keep the extender wrapped closely to the tires surface, even though it would give more
protection if it extended straight down from the fender.