I had a look in the codebase and yeah, the code has been completely removed so they're completely gone, they're not just disabled.
The reasoning for removing stuff I remember at least, I never was happy with how the code basically needed a completely separate copy of the behavior for each axis (applying to both rendering and collision). Rotating cylinder objects in a prefab/copypaste didn't work as expected either (since they would have a rotated size but still be cylindric along the original axis) and starting to need special behavior for rotating certain objects felt like such a kludge I just couldn't keep going anymore. And the collision code for tunnels especially always was a nightmare, they are paper-thin so for smaller tunnels it was easy to get stuck, and there was no good way to connect tunnels to a start point or a corner that LOOKED right (for making sewers etc) so I always felt like they were a total failure. For making tunnel areas I'd recommend using separate prisms for the floor and ceiling instead, they even can be cobbled together into smooth rounded corners.
There's no way to rotate things around other axes. A lot of stuff treats the vertical axis in a special way (since Game Maker doesn't have a Z axis natively) so a lot of code (especially the collision code) wouldn't know what to do with e.g. a prism protruding along the X axis instead of at the top.