You're right. If you have the freedom to choose the best tool, I think you absolutely should.
I think the problem lies in the fact many programmers don't have the luxury of making those decisions. I imagine if one of those programmers refused to use the mandated tools, they'd get the sack. Many of those programmers, again, don't have the leg room to handle that. Plus, I don't think any employer would look favourably on "I got sacked because I refused to use language X because language Y is superior". I know that isn't the kind of attitude to work I would appreciate.
The companies that allow freedom of choice in tools and languages are perhaps the best companies to work for. Unfortunately, those companies hire the best programmers in the first place, or at least set the bar with that in mind. Most programmers, including myself, are not of this calibre.