Fully agreed. This is the most important point. No company or vendor should prevent me from running the software I want, in the way I want, be it modified for my own purposes or not.
Sure, if you only look onto the security side it may be more secure if you can only run approved software, but it is in no circumstances okay to reduce the freedom of a user on his/her private machine. (In a business setting it makes sense to only allow software approved by the IT-Department)