Though for this specific vaccine the question is somewhat irrelevant. In this case, they are introducing an antigen that the underlying condition, MS would never cause to occur. This antigen activates regulatory cells which then supress the immune systems production of myelin targeting antibodies.
So in the case eof a normal vaccine, regardless of whether it is mRNA or not, the vaccine is conveying information to the immune system that you might also acquire through an active infection.
This vaccine however is conveying information to your immune system that no active infection would convey.
This all kind of answers my own question which would seem to be yes. As long as they can find an autoantigen that will stimulate regulatory cells which supress the problematic autoantibody producing immune cells. At least that is my read after mucking through the medical jargon.
mRNA is tech that BioNTech is developing is completely digital. Once you have the RNA structure in the computer, you can just "print out" drug/vaccine using the same process without changing anything else.