Not familiar with the versions of MC that use a marking tape--would it be feasible to keep the marking tape intact and route it with the conductors through the EMT?
As a practical matter, if you have MC cable with marking tape that terminates directly to a box, is the marking tape visible from within the box? If not, then removing the marking tape and routing the conductors through some EMT doesn't yield any difference in identifying information available after the installation is complete.
In other words, if the marking tape's job is just to provide the identification of conductors at the time of installation, rather than at some future time, it does that job equally well when the MC terminates directly to a box as when the MC is transitioned to EMT with the marking tape removed. Either way the installer can look at the marking tape and confirm the identity of the conductors.
Cheers, Wayne