It does for me, select the item in the scene tab, select the alt UV set in the surfaces tab, in DS3 it save as material preset, in DS4 it save as depreciated material preset, write out the file name and select the file type (DSA & DSB in DS3, only DSA in DS4), on the next window, you should see record everything with a check mark next to it, bottom left of the window you see a check box next the words "Save alternate UVs", tick it and select Accept.

Your alt UV's will now be in the DSA/DSB file and will automatically be used when you apply the preset to your item, I've been applying M4 textures to V4 (and vice versa) this way for quite some time.