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I think the main reason tables are included in extensions, rather than in the CommonMark core, is that the original Markdown syntax by John Gruber did not include tables at all. Many other flavors and implementations of Markdown don’t include tables either, not even basic ones with pipes and hyphens.
There’s something to that. I suggested something similar as a mostly-least-common-denominator approach. On the other hand, I would worry about trying to impose any sort of table standard where none exists.
CommonMark isn’t quite a “standards committee,” it’s really just yet another Markdown flavor, but even so I feel our main goal is to specify rather than to innovate. Given the huge variety of table syntaxes and potential conflicts, it might better to step back and let the major players fight it out as the de-facto-standardization process runs its course.