Did fishing-fleet guard ships fall under the trawler command?

Did the guard ships watching fishing fleets fall under the trawler command as well?

Yes. Most of those guard ships were converted trawlers.

Most of the guard ships used for watching the fishing fleets were converted trawlers. That places them within the same wartime patrol system whose vessels were counted separately from the Royal Navy's roughly six hundred full warships. Commercial hulls could therefore expand local guard and patrol coverage without consuming scarce purpose-built combatants. The exchange also explains why headline warship totals understate the size of Britain's naval effort in World War I.