Do you know if there is any selective agar for both of the strains? Or conditions that make the growth of one permissive while one not?

If that's the case, the only way I can think of doing it (outside of staining/phenotype analysis and what not) is growing up a non-selective condition and after growth inoculating that growth identically onto the two different conditions (I'm imagining the Velvet-transfer done by Joshua Lederberg for the early experiments in bacterial conjugation. Old school but highly effective). That way you can get a count fairly easily.

Not sure if that helps, but maybe it can jog a few ideas in your brain.

Thanks Kenneth. As far as I know, there are no selective or differential agars that can do the job. I think we may have to look at a combination of temperature, pH and water activity to selectively count these bacteria.