you should be specific about which C spec you are referring to, you talk about "the C spec" and then you mention the "pre-C99 implementation". Maybe you mean they've always been illegal in every version, but it would be more clear.
I don't get all the programmers that scandalize if you use GNU extensions, they are fine, and mostly useful, so if you are using GCC to program I don't see why not use -std=gnu11 instead of -std=c11... who cares if the program is not compliant?
Even if you want to be compliant to share code, the C standard is you last problem, the thing is that you probably use a ton of libraries and header files specific to that implementation (such as POSIX or even worse Linux-specific stuff), so your code is 99% not portable anyway without rewriting most of it.
[1] IIRC on OSX[2] gcc actually invokes clang
[2] stopped upgrading before it became macOS
It's saying that C99 implemented flexible array members but before then some compilers introduced their own (nonstandard) implementation of flexible array members, using the (not allowed) zero sized array notation.
1. Pre-C99, no flexible array was allowed.
2. Gradually, people started using the "size-1 array at the end of a sturct but write beyond" hack as flexible array.
3. As an attempt to do the hack in a more ordered manner, some compilers, including GCC, started officially supporting the non-standard "size-0" array extension.
4. C99 added flexible array with indefinite length (array[]), while prohibiting both the undefined-behavior "array[1]" and the non-standard extentios "array[0]".
So when people say "size-0" array, it could mean either of these three things, and it does get a bit confusing. But fundamentally the idea was the same, all of the three techniques are used to achieve the same practical effect.