Six versus twelve saddles is personal and subjective. At home, and all alone, my 360/12 with a 6-saddle bridge was very pleasing to my ear. Then I played it with my band and could never get it to blend with the two other guitars to my satisfaction. I ordered the 12-saddle, installed it, and for the past four years it has always made me happy and has sounded excellent when played along with my bandmates.
This observation of your guitar with the 6 saddle verses the 12 definitely has merit!
Although some 12 string guitars with 6 saddle may blend OK with other instruments, it is a safe bet to say in the majority of examples a 12 saddle will intonate more successfully. Good to know ''your in tune'' too or at least your ear that is.