I have always believed that referring to a Senior Officer as "Sir" is the proper address for both males and females in most military situations.
However, an increasing number of comments I get on Foundry missions run the gamut of "My character isn't a male. Dont call me Sir" , "Not all characters are men. be more gender neutral", "Sir" isn't how I would refer to my female officer" , etc etc etc
So what is it ?
I believe that addressing a senior officer as "Sir" is in fact , gender neutral.
Spock : "Very Well, MISTER Saavik. you may Clear all moorings"
"Take her out MISTER Saavik"
From Military Website :
However, recruits of the United States Marine Corps and United States Coast Guard address both male and female commissioned and non-commissioned officers as "sir" in basic training, especially drill instructors (USMC) and company commanders (USCG). Enlisted members of the United States Military always address Commissioned Officers as "sir". During training "sir" is implied and will be replaced by the rank and grade of those addressed after initial indoctrination.
Sir if fine. it might be cutting it a bit fine at times but sometimes players expect foundry authors to jump through hoops for them.
if you start using the rank command people will get upset that they roleplay a captain even though their rank is admiral. you use captain, they will get upset you dont use their real rank. honestly it never ends.
I knew I'd remembered something about this from Voyager.
From the thing you quoted :
Janeway: "Ensign, despite Starfleet protocol, I don't like being addressed as 'sir.'"
This would seem to indicate that SIR is indeed Starfleet protocol. Being addressed otherwise was a personal choice by Janeway. As authors we cannot account for your "personal choices" about how you want to be addressed.
It IS seemingly "Starfleet Protocol" to call senior officers, SIR. So, it seems a safe approach to use established Starfleet Protocol.