A lot of the GNU tools have had dependencies on GNU-specific versions of classic tools because, for decades, the non-GNU versions sucked. Lots of hard-coded arbitrary limits (line lengths, file sizes, command line option counts), quadratic behaviours, crashes, weird corner cases.

Edit - also, lack of updates. POSIX added a new feature to a tool 5 years ago? Well, the built-in tool that came with your classic Unix probably still doesn't support it yet. The GNU tool does though.

If your build system effectively relies on GNU `make` because 75% of the other `make` implementations out there either barf on your makefile, or don't run the build steps correctly, despite it being valid according to the spec; and GNU `make` has a bunch of features that are really powerful and would allow you do some complex things more easily, or even do them at all; then why not just actually rely on GNU `make` and use the extensions?

Similarly, the bundled `cc`s with classic Unices (if they were provided at all) frequently had weird bugs or poor code generation that would go unfixed for years. If `gcc` was the only compiler you could rely on a) your users having access to, and b) to correctly compile your code; and it has a bunch of really cool features that make your code smaller or faster or cleaner, it's hard to resist that. Your code is still portable, because `gcc` is portable, and Free.