Warning appears if multiple namespaces contain the same custom Composer script name about composer-bin-plugin HOT 2 CLOSED

That is correct. The only way to "fix" this is to specify an order in which the bin directories should be installed but even so I'm not sure it would 100% work. For example if you have:

namespace1
codesniffer <- the main you want
phpstan <- because it's a dep, not because you are interested in
namespace2
phpstan <- the one you want

in this case even if namespace1 is guaranteed to be installed first (because you would have an option to), the symlink for phpstan would not be the one you want.

This is why I highly recommend to disable symlinks. The path to pick is a bit less convenient but it completely avoids this sort of problem.

from composer-bin-plugin.

I've disabled symlinks from the beginning I started working with Composer Bin Plugin. But the warning mentioned above appears nevertheless:

Main composer.json:

"extra": {
    "bamarni-bin": {
        "bin-links": false
    }
}

from composer-bin-plugin.