Not necessarily. In actual fact, this is how things are done in the public service. There are unilingual francophone regions; in other regions, anglophones and francophones have the right to work in their own language. Then, there are regions where anglophones are not required to speak and understand French.
To some extent, this is a parallel approach to the one adopted by the public service. However, I share your concerns as to what this might mean for a mechanic or another francophone tradesman, who has to transfer to another unit.
If I understand correctly, the intent is to avoid the situation you've described, of a francophone soldier with a senior officer who doesn't understand French.