The main difference is in the way that Acunetix is installed. The Windows version can be installed using the GUI installer, while the Linux version can be installed from Terminal. The Acunetix web UI is the same on Windows and Linux, and the same functionality is to be expected on both operating systems.
We are making some updates to the way that Login Sequences are recorded. In the meantime, you need to launch the Acunetix Login Sequence Recorder from Terminal as explained here