I think the problem is very much like NOAA SAME Alerts. The NOAA Alerts and/or Fire Tones are short in duration (usually 10 seconds or less) and if the scanner is off scanning multiple systems and/or listening or stopped on traffic for a different system, then the Fire Tones will most likely be missed.
Since you are mentioning Fire Tones, assume you are dealing with a non APCO digital system? If this is the case, as mentioned, I would dedicate a scanner for the specific Fire channel with Fire Tones. You can likely purchase a used analog scanner for a reasonable price and dedicate the scanner to this task.
If I wanted to ensure my scanner receives fire dispatching "stuff" while I was doing "regular" scanning, I'd set up priority scanning with the fire dispatch frequency being a priority channel. I might even think about programming the alert light and an alert tone for that channel.
How the Fire Tone Out deal works with respect to general scanning makes perfect sense to me. It's the difference between "Active" and "Passive" scanning.
"Active" is where I'm awake and paying a decent bit of attention to my scanner. By setting priorities, I'll hear fire dispatches with the rest of the stuff.
"Passive" scanning is where I might be doing something else like sleeping or watching TV. In that case I'm only interested in re-directing my attention to the scanner if something specific is happening, such as a fire call.
What would make sense to me is the ability to weather alert scanning and Fire Tone Out at the same time, if it was technologically possible. Fortunately around my community, if there is bad weather, the fire dispatch center will activate pagers, so if I'm in Fire Tone Out, I'll still hear about bad weather moving in.