Just almost too many caveats to mention. Be sure to check your manual to make sure what size it will handle, it should be in the specs. One of ours will handle 2 1/2 and the other 3" which we regularly cut by lowering the front bucket and knocking them down to protect the cab glass.
We use the front bucket as a "feeler" in rough stuff and it has saved the cutter by locating stumps etc. I have also used the FEL to get out of a washout that appeared over the winter months.
As mentioned, you can back over stuff and lower your cutter, but in backing over stuff, you are putting your tires right on the freshly cut stobs which may or may not be a problem depending on how low you cut. Going any distance in reverse can also be pretty tiring. I do this on occasion depending on what I am cutting. We use a pull type Woods DS1260 which is hard to back straight without turning around or using mirrors. I also use a 6' Land Pride RCR2672 and routinely run over stuff up to ten feet or more tall. I have managed to tear the boots up on my Kubota tie rods, but they are easy to replace and some tractors don't have them so exposed.
I know of no rotary cutter that won't handle 1" saplings though they may exist, I cut them that big with my little BX and 4' cutter.
As mentioned, if you don't have a slip clutch carry some extra shear pins and if you have a slip clutch make sure it is properly adjusted.
Check to make sure your blades are properly "sharpened", ie as per manual which should be a square profile of about 1/16th of an inch with square ends I think, check your manual, there is a thread on this somewhere.
Keep your hand on or near your lift in case you get into something you shouldn't or be prepared to shut it down nd disengage the PTO.
I am sure there are others I am missing, but other members will catch them and bring it up.
Here are some pictures of stuff we cut.