There was a certain degree of protocol in referring to military men. “Mister” was used to refer to Subalterns (Lieutenants, Ensigns and Coronets) in the Army, and Midshipmen in the Navy. Possibly it could also be used for various other positions (Surgeon, Paymasters, etc.) which today would be considered “Warrant Ranks”.

An Army Captain, or a naval Lieutenant, or anybody recently making rank just slightly above Subaltern/Midshipman might take it as an insult. That is, they are not being recognized for having made the jump to full command status. On the other hand, by the time one reaches Field (Major, Colonel) or Post rank one might feel a great deal more secure about their status.

In Colonel Brandon’s case, he is also a “Mister.” He owns an estate and as such likely has many other non-military roles. Being retired does not necessarily change how he would be addressed. Former officers (above the “Mister” ranks) often continued to be addressed as such into old age. I think General Tilney would decline being addressed as anything but up until his final breath.

Marianne’s use of “Mister” might also reflect her seeing him differently than most people.