I misspoke: the problem occurs when encapsulating the git command with monospace. The literal block does indeed behave correctly.
See below for example. Both docbook5 and html output convert user@server.com to an email address.
MT
--
= Git URL Test
First Last <first.last@company.com>
This document tests the rendering of git url's.
Git clone command with just server name shows up *correctly* as `git clone user@server:repo`.
Git clone command with domain shows up *incorrectly* with email address as `git clone user@server.com:repo`.
Literal block does behave correctly with domain:
....
git clone user@server.com:repo
....