is the "The TMS can't handle 6 cars" a fundamental hard wired thing or a "software problem that could be sorted of money was thrown at it"? It may be the sort of thing that's not worth it for a penny-pinching SE with 36 units but may, if the platform length issues of the ELL can be overcome, be viable if TfL had 57 378s and 36 376 all wanting an extra carriage.
I believe that it is a hard wired thing, and whilst there is a fix (the 2 semi-permanent 3 car halves) it is a) not cheap, and b) asking Bombardier to deal with a design that has not been in production for quite a while, and that will also carry a hefty surcharge.