That is nice and all, but there's a few issues.
1. If the craft is damaged and out of fuel, then the craft is unusable until the repairs finish, which can take a long time.
2. If the craft is damaged and out of ammo, then the craft is useless (as an interceptor) until the repairs finish, which can take a long time.
In my opinion, these are not issues, but desired and well designed fundamental geoscape features.
If the player/modder would be practically able to work around all of the limitations, then I could also just remove all of this. Features that can be ignored and have little to no impact on gameplay, are just fluff. And I'm not interested in fluff.
If you want additional "lore/fluff/canon" justification, think of it as craft damage being split into two components: damage that prevents a craft takeoff and damage that doesn't prevent craft takeoff. Xcom only shows you the first component, the critical damage. All non-critical damage is not shown to you, and the good engineers at the base continue repairing the craft whenever they can, without bothering the commander.
What I am willing to make configurable, if the modders (not players) are interested, is how long it takes to fully repair a craft. Currently the formula is simple, and depends only on one parameter, the repair rate per hour. I can imagine adding more parameters, like for example number of engineers at the base, or a presence of advanced hangar, or something like that. Of course, there would still be some hardcoded minimum possible duration, so that it is not possible to turn this feature off completely. (And yes, it is possible to turn it off completely today, by setting some crazy repair rate, but as far as I know, no modder has ever done that, so I don't have any reason to interfere. Also it enforces my belief that non-negligible and non-avoidable craft repair times are a desired feature.)
All that said, I'll repeat that this is just my opinion, feel free to disagree with me.