It seems that over the past year, about 6 in 10 wmf branches are created by someone who does this, and the other 4 by someone who doesn't.
Whenever the wmf branch is created in a way that leaves the submodule changes local and uncommitted, it means that for a full week, the git status output in /srv/mediawiki-staging/php-x.y.z` is "dirty" by default.
This means people that watch this carefully (or that have an enhanced PS1 git prompts that includes this information), have to double-check the verbose version of the status for every action they perform in that directory.
It also means that for people who watch it slightly less carefully, are likely to ignore it due to "banner fatigue" from it being dirty by default that week (this has led to numerous failed deployments due to an extension patch not actually having been deployed).
I've assumed thus far that on weeks when it isn't committed, that it is due to oversight, but a recent IRC chat made me conclude that it's just not something well-documented and newer operators probably never learned it.
Given git status has been dirty for two weeks in a row, filing this as a train blocker. For the next train, please commit the submodule updates. I don't know with what level of automation or manual steps it needs to be done, but please ensure the git status is clean in the new branches going forward so that others can also deploy with ease and confidence.