The addon SDK may be limited. I appreciate that. However I suspect most of the time, there are workarounds to what you want to do. I'm pretty sure at least some of the time you don't have to go hack the engine. As I mentioned, with a traditional native engine, usually there is no scope to hack the core engine at runtime, and so everyone resorts to other workarounds and gets by; only JavaScript makes it easy for people to hack the engine at runtime in this way. I get the impression people realize they can, and then they reach for it as their first solution when there are better options. There is also the feature request system, which I also appreciate is slow, but that's the official way to get new things supported.
Sure, if an engine has an open source runtime, you can hack it to your heart's content. But as I explained before, that's a double-edged sword: you could well end up in development hell, and some people learn that the hard way. Someone giving you source code doesn't mean they'll support you if they make a mess, it's more just "here you go, good luck".
do you plan to obfuscate the whole undocumented runtime and only let us use the documented features ?
There is this warning in the addon SDK documentation:
That warning is there precisely because it is a real possibility! It could happen unintentionally, it could happen because of some major upgrade or new feature, or it could happen because we want to improve encapsulation for better long-term reliability. We don't want to break things, but the point of this warning is if you use unsupported things, it definitely can; we will do our best to avoid causing major disruption where reasonable, but it may be infeasible or go against our long term plans, in which case, what can I say other than we tried to warn you?
If you ignore that warning, you should be working under the assumption that the undocumented features you are using can change or be removed at any time, just as it says. I would say if you are going to ignore that warning, the only responsible way is to have a plan in place for what you are going to do if the thing it warns you about then happens, so then you can fall back on plan B. But then in that case I would say, just do plan B first, and you won't have the trouble with undocumented stuff changing or disappearing.