Adding a reference to a command results in a horrible layout where the link is formatted as its own paragraph. See tl-sso-token-passphrase for an example.
Specifically, an example is found in rev 14518.
We've now switched to reStructuredText and Sphinx in bug 4951, so this is no longer relevant. References work fine there no matter the target. (Note that commands aren't currently cross referenced, see bug 7783)