Before we wander to far from the OP....
Based on the OP, & how I envision what he described and IMHO, the wiring method perhaps should have been a raceway, not MC.
As to 'bonding' the EMT, it's not 'structural metal', it's a raceway. The short section is a gray area, as Greg said...define 'short'.
Again, IMHO a concern of phy. dam. to the MC? Terminate and go with a raceway.
