Why no specific script: to avoid maintenance hell,  which you get when you start making more and more copies of basically the same thing. 
Basically that's also one of the reasons why not to use script in project root. The script might change -  for whatever reason -  in RMT.  If you use the vendor/bin/RMT Symlink the script will be updated on composer update on the RMT package.  A local copy won't. 
As I mentioned before if you use default behaviour the RMT file in your project root is still the same as it was, see the change in the InitCommand class. 
Your example with the bin folder does not make much sense to me, since the script is not in any bin folder. If you use the local RMT this script is only ever called when a) you guys make a new release of RMT, which I would assume you do when being in project root,  and b) when calling vendor/bin/init (that's the new one), which is to avoid having to add the command.php to vendor/bin as well (calling that file directly for init is the workaround you are having in the docs most likely because __DIR__ is not working.) not sure how you want to use a config location to determine where to write the config.