Obsidian tries to stick to commonmark. Off the top of my head there are two additions (wikilinks and comments) and one difference (for performance, an HTML block must be contained in one markdown block). Other differences are due parsers bugs and will eventually be addressed.
If the incompatibility with other tools is due an Obsidian deviation from Commonmark, you can file a bug report and it will be threated as a bug.
If the incompatibility with other tools is due to other reasons, you can open a feature request and it will be voted/evaluated on a case by case basis.