I just took another look at the Shapeshifter manual, and it does in fact seem to have a simple envelope if you put it in “Percussion Mode”. You can send your gate signal into the sync/trig input and it will give you a simple AD envelope on the output amplitude. As the name implies this envelope is mainly for percussive sounds but nothing stops you from giving it a long decay tail. What you can not do is use the OT sequencer to control the duration of that AD envelope because it doesn’t have a sustain part.
You can also send the Shapeshifter into the external VCO input of the Atlantis as you said. This will give you only one voice, but a very thick sounding one.
What you can also do if you use Yarns in 2 Voice mode is send a CC from the OT into Yarns and use that CV output as an extra LFO/envelope to modulate parameters on the Shapeshifter.