The Tavern

Playing a White Draconian who has the Poison Spit mutation.

Conceivably, the sources for these come from different bodily places, yet the Breath recharge penalty applies to both.
Translation : If I spit posion, get the breath status and therefore can't breathe ice and vice-versa.

It means you don't have a bunch of different cooldowns to juggle (and you don't have a bunch of different Breath indicators to display).

And you only have one pair of lungs.

I would be in favor of limiting mutations to one breath weapon at a time.

It's kind of cool in a three-wolf-moon way that golden dragons can breath fire OR ice, and it appeals to me that rare characters can develop multiple breath weapons. It doesn't double your firepower, since you can't use 'em both at the same time, but it gives you a decision about which to use. Do you use the fire breath on the zombie in the front, or save your breath so you can use poison on the susceptible spider behind it? Taking away multiple breath (or adding multiple timers) is taking away a fun decision, albeit a rarely relevant one.

Draconian priests run into similar issues.

The extra versatility is rarely interesting though. By the time you get multiple breaths, it will probably be too weak to bother with 99% of the time, unless you somehow got multiple levels of both breaths. It basically just acts as a filler for when you want to gain or lose a mutation. The correct answer to your jejorda2's scenario is to use fire now if the zombie is close, and just use needles on the spider.