Replying to my own post: I just suppressed one part and drew one just like it from a new part inside the assembly. That part did save as transparent in the EASM file so it looks like the problem has something to do with the fact that it was from a pack and go assembly. Hopefully there is a solution to this so I don't need to draw 16 of these from scratch.
Edited to add: At least there is a workaround. By changing the material of the parts in question from 6061 to ABS PC before saving the eDrawing, they will save as transparent. I'll leave this up so hopefully it helps someone.
Well I spoke to soon. That workaround helps some times but not always.......