Does LensAlign work for manual focus lenses?

It is more that you can test the manual focus than calibrate it. The major point being that most people just assume that manual focus is accurate. But this is far from the truth for any number of reasons, including but not limited to:

Modern focus screens are not designed for focusing...just to be bright.
The DOF in the viewfinder is more than the lens is wide open also making it harder to focus
mfg tolerances in the placement of the mirror, focus screen, pentaprism or penta-mirror
photographers eyesight and eye hand coordination
diopter setting
and more...
With LensAlign you can focus manually on the focus screen to the best of your ability and given the obstacles above, to attempt to achieve best focus. The results are displayed on the focus display ruler, and the accuracy of the manual focus (including the photographer as a variable) can be quantified.

To the degree that it can be calibrated, many photographers, given the knowledge gained from the testing, can learn to focus a little off from the focus shown in the VF thereby achieving proper focus. Also the normal AF system adjustment, will calibrate the AF confirmation light, which can also be used as an aid in manual focusing.

Hope this helps your understanding.