I agree it would be nice if apt worked like other distros but it has never been that way. I don't believe apt could be removed due to to HAM depending on it.

Interestingly apt in maemo is a modified version which hides packages with user/hidden category. From what I recall this was used by offscreen nokia apps in the non-free repo, way back in the day.

There is more to the package management in Maemo than dpkg and apt. HAM uses domains as an extra check on packages.

Take your example of apt in extras, using domains your apt package would actually be the latest version in the root filesystem repository (SSU) and should not be replaced by any "rogue" version uploaded to extras-devel or any other random repo with a greater package version.
Unless you installed this other version manually with apt breaking this "feature".

Really the "disclaimer" should be on rootsh or having root control of your system with R&D mode.
Do you want to be stopped from having root access to your device? Looking at the bigger picture removing that from extras would simply fix the issue if you think about it.