I can see some points to both sides of the argument. (For reference, "STS" where it appears below indicates the phrase "standard tool set," referring to a uniform set of tools on a system.)
Having an STS to work with makes it easier to set up new systems, handle updates, and troubleshoot issues. It also makes it easier for anyone to interchange machines (whether temporarily or on a more permanent basis), and having a standard configuration for those tools in the STS can make things such as applying a standard coding style easier, which in turn can make life easier for things such as CVS repositories. (Yes, I know about things like PerlTidy, just pointing out the logic.) In addition, having an STS means that a new person doesn't have to wonder where to get a tool to do (fill in blank) function.
The other side of the coin that I see is that many people, while competent enough to use other tools when necessary, have a set of tools that they are the most productive with. The ability to do function (fill in blank) in one tool may be something they use extensively, but may not be used by (or may even be missing) from a tool in the STS.
Having said that, the former view can lead some to assume that programs can be written in assembly-line, cookie-cutter fashion, while the latter view to the idea of the programmer as an aloof artist who slaps code on a phosphorescent canvas with a brush. While I think some engineering/scientific/mathematical principles can be useful in the development process, I still find it to often include just as much of artistry and craftsmanship.
The best compromise I see is to provide an STS (maybe even with more than one tool that does the same function, if there is enough desire for it, such as providing both vi and Emacs), but allow programmers to use other tools if it improves their productivity (I am ignoring such administrativia as licensing and such, for this discussion), and to allow suggestions and evaluations of other tools for inclusion in the STS, especially if the people having to use them do so for very different circumstances (such as someone writing *nix/perl code in a department with persons writing database queries or ASP/PHP/HTML).
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