the Pro 90 will go down to slightly thinner metal, ie, car thickness after being brushed with a flap-disk where the 100 will be slightly more prone to blowing holes.
On the other hand the 100 will allow you to work on slightly thicker stuff if you should ever need to, ie, chassis rails.
The 90 /will/ shut down due to overheating and it /will/ annoy you unless you fit an extra cooling fan. The 100 won't be quite so annoying but would still be better with a fan attached.