Hmmm . . . as a test I just imported two .mov files with transparency, one a ProRes 4444 file and one in Animation codec. Both files imported fine, but the transparency of the files was not supported when placed above another clip in Rush.
Videos with alpha channel transparency can be ProRes 4444 or Animation or PNG or similar image sequences, all of which aren't supported on iOS.
I've tested videos with both ProRes 4444 and Animation codecs with transparency on the desktop version of Rush and they work fine on top of normal videos.
When trying to import these codecs on the iPad or iPhone version of Rush - you get error messages (unsupported file). You also generally get an error message when trying to save these types of files onto Camera Roll or Files on an iOS device. iMovie, Magisto or Clip won't take them. LumaFusion seems to take them, but not play them back properly. In fact, they come with an error message saying the files are not entirely supported.
I think the solution would be for Adobe to integrate a way to import 'Motion Graphics Templates' created in After Effects and or Premiere Pro into Rush.