Why do these two values reset to 0 as soon as I set them?
If I need to use the Failsafe return to home is it going to crash because this value is alwas 0?
The value that you set in the App while connected to the P3 will remain with the P3 regardless of what shows on the App. It is a known bug in the App but it does not effect the RTH performance of the P3.
I just tested RTH with my P3P and it worked flawlessly. The P3P climbed to the preset altitude, flew overheard of the RTH location, then descended and landed, all without incident.