I'm not on top of the nightly builds either, as I always compile from source.
Jasem's ubuntu builds are here:
launchpad.net/~mutlaqja/+archive/ubuntu/...field.series_filter=

The way the alignment works is that the system works out the altitude and azimuth angular offset of the mount's axis from the pole.
The UI then gives you a target position and asks you to adjust the "altitude knob" to correct the altitude offset,
then the "azimuth knob" to correct the azimuth offset.
As you point out, the mount may not be perfectly level, so this isn't entirely true. However, unless you're wildly out-of-level,
I think it would be reasonably effective anyway.

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