Try as I might, I cannot reproduce this in a test instance hosted by yourselves.
The on screen description is the same (HEAD -> master), but the actual URL it goes to is different compared to my instance, even with the same repositories loaded.

1. Install Phabricator at the version noted above.
2. Import a GIT repository via observing a URI.
3. Note the reference HEAD -> master link broken on latest commit.

You're correct, using brackets makes the regex work, thanks.

In T5301#149071, @epriestley wrote:

T5397 is another copy of the pipes-in-tables issue.

You can use remarkup.ignored-object-names to prevent S3 from being marked up: S1 S2 S3 S4