Don't need AWD to rally
The transmission has little to no affect on emissions. The take rate for manual transmission vehicles is so low, that makers save money by not even having it as an option on vehicle. The Jeep Renegade is a prime example. The Renegade could be had with a 6-speed manual up until 2018. The take rate for manual Renegades was under 10%. So they dropped the option and kept the auto. Also, auto transmissions are becoming faster to drive, and more efficient than the standard manual transmission. Gone are the days where the manual option is the "fastest" and "most fuel efficient" economical option.
P.S.-Focus ST is FWD, the RS trim is the AWD variant. And just because they share similar DNA, does not mean a manual swap is easy peasy. In reality, the similarities are in the suspension. That's about the extent of it. The van benefits from having a low flat floor for either great access to seats for the wagon, or plentiful flat space for cargo. To implement AWD, you will need a transmission tunnel larger than the one already underneath for the exhaust system. This means the tunnel needs to expand and potentially raise the floor, or the drive train sits low and exposed to that one speed hump that's abnormally larger than the rest.
Is it possible? absolutely. There are more than a few manual swaps done to both generation of TC.