I have just returned to home to PA after a once in a lifetime trip on pursit of native trouts.
The Gila is one of the trouts that I did not pursue because the streams were more remote than I as as a solo party wanted to undertake- 5-7 mile hike each way or the were just plain stocked into waters. I was into fishing for natives or as much as possible.
Also, a very limited number of waters open to angling. If I recall correct one of the states has closed angling for it- like you pointed out , fires can wipe out whole stream pops.
One potential danger that really sunk in out in CA, AZ was the potential for crazy flooding. Lots of washed out roads etc in evidence.
I did have the chance to catch a native Apache trout. During the trip it was pretty common to have to hike 2 to 4 miles in the head water streams to get to where the native fish of been pushed to Also the size of the streams were very similar to brookie streams here in PA.
The best advice in pursuit of fish is so your homework/ planning because as you pointed out these streams can change drastically year over year. And call the local biologist, they will tell exactly where you can go for best chance of angling. They spent 30 mins on the phone with me , they were very accommodating to my questions.
Wild thing about Apache trout is the have a spot before and behind the eye- looks like sorta a bandit.