I like the sound of it reducing stacks over time rather than it outright blocking fire damage. It would almost free up engineers from putting out fires if the fires weren't heavy enough but the downside would be that fire would always do damage and chem spray wouldn't put fires out directly. It would pretty much force fire wielders to lay it on heavy and hard and this would in turn work well with the new fire stack icons/markers.
What if instead of applying retroactively it applied proactively? Say it granted parts a 50-75% chance to resist fire. In effect, you'd reduce incoming Flamethrower fire chance (per particle) from about 24% to 6-12%, depending where the actual numbers fall. A Flare Gun might only apply 3-5 stacks of fire instead of 10.
You could get away with a slightly longer buff time AND with keeping the actual extinguishing numbers low (even at the 3 it currently is), and it would be balanced out by the reduced (but not removed) chance of accruing fire stacks in the first place.
It gives both tools a more defined role: Extinguisher is raw extinguishing power, Chem Spray is safety at the expense of knowing that continual exposure to fire (sitting in a flamethrower, for example) will eventually spiral out of control.
The percentage could also scale down either over time, or with fire stacks: Maybe something like resist equal to (70% - 3% per current stack on the component), so that the Chem Spray is better for short engagements vs. fire, but definitively worse against long exposure.