It is always possible that the pre-installed packages by Dreamhost (and trust me, that’s a lot of them) will be ‘managed’ by dreamhost as well. But that also means it won’t stay up-to-date constantly. I for one, removed all the default pre-installed packages by dreamhost and re-installed the required packages manually to keep things up-to-date as I see fit.
The downside by doing this is that the control panel stuff (like php, apache, etc settings) will break down and it’ll no longer be a full ‘managed’ VPS. The only thing that still works on our end is the MySQL databases but that’s only because the SQL database is on their end, and not on your own VPS. (in short, MySQL server is not installed, only MySQL client).