Hello, welcome back to the forums!
I am not entirely clear about your problem: the old 11.x release builds of what was then called Simutrans-Experimental (now Simutrans-Extended) are long deprecated. The correct latest builds are the nightly builds, available here
for both Windows and Linux. These latest builds do indeed support half height slopes.
The latest nightly builds will work with paksets old and new, but the newer paksets that support half-heights will only work with the new version of the executables.
As to the library issue, the nightly builds are compiled using Ubuntu 16.04, so they should be using very recent libraries. You can always compile from sources yourself if you are having trouble (use the master branch), and that is generally fairly straightforward on Linux. I should note that the .deb package has the exact same executable as is available separately.
I presume that you are running a 64-bit system?