It's been quite a while, so I'm going to rehash a few things:
Firstly, I know that people want to change their keys at will, and I am aware at how unusual it is for there to be "hard-coded" keys in modern games. I'm also aware that many people want to argue: "You can do it with a mod, so..."
But, returning to what the devs have said several times in the past:
They do not recommend that you change the hard-coded keys, as it can cause issues.
How -- why -- what are the details --? No idea. That's never been explained, but this has been the case in TW1, TW2, TW3, and now CP2077. What's the common factor?
REDengine.
Thus, it's fairly safe to deduce that something in REDengine relies on certain key inputs for certain things. Regardless of how "stupid" that may sound to a human, computers aren't humans. Engines are mathematical processes, and I don't need to explain what happens if you fail to "carry a 1" while doing a huge equation. If it's deeply rooted in the engine, fixing it may simply not be feasible or even practical.
Also, just because a mod can get around it, that does not mean that it's safe. Again, the devs have recommended people not change those keys. Mod authors will very often do things that introduce bugs, large or small, without meaning to, and without the larger player base ever recognizing that it was that mod that broke something. This is passingly common in modding. Even if the mod works perfectly fine for you -- that doesn't mean that it didn't completely destroy another player's game. Mod authors don't have access to the source code, and they can't possibly be held accountable for that if their mod does create an issue in players' games. As always, you use mods at your own risk.
Companies do have access to their source code. Hence, if they know that something may very well create an issue, they will prevent it -- regardless of how "stupid" or "ridiculous" that may seem to the player base.
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In the end, nothing with this issue has changed. Once the keybinding mod is updated to the latest version of the game, I'm sure it will work fine again. Knock yourselves out! From the sound of it, it's mostly fine. But the devs have not announced anything different on the "not recommended" front.
If you use the mod, you do so at your own risk. I know of no plans to allow the hard-coded keys to be rebound within the game itself.