The alternative is to not have (most of them) at all.
The reality is that 99.5% of users have perhaps 10 or 20 actual usecases/requrements. - You named a few of the most prominent ones. These need to be supported (e.g. with flags) and documented properly. Everything else is excess can be removed.
The problem with this is: You need to find out what users want to do. But many software projects are just too lazy and push all the effort downstream.
For all sorts of testing reasons, there has to be a way to disable the JIT. There has to be a way to disable sandboxing. There has to be a way to bypass the GPU acceleration blacklist, and there has to be a way to forcibly disable GPU acceleration regardless of the blacklist. Thank god the options exist!
I mostly just wish the documentation was better. It would be really nice if I could filter the flags by platform. And, well, they should probably live somewhere other than this web page.