I am a little confused by this post.
Regading Obsdian Core,
Wikilinks are not part of the markdown spec [[link]], However, I believe they will eventually be included. If you are concerted about it, use standard markdown links.
Since wikilinks are not part of markdown, that’s even truer regarding header/block-links.
nested tags in YAML I am not sure what you are referring here. Tags (nested or not, in yaml or main text) are not part of the markdown spec.
embeds - what do you mean by this?
I am not sure I fully grasp your problem.
I will approach this from another angle.
Obsidian strives to support markdown 100% and be commonmark compliant.
Yes, there are augmentations (but not modifications) to markdown (e.g. handling tags or using wikilinks).
Plugins can add even more stuff in form of specialized codeblocks (add not modify).
I would like to point out that dataview, tasks, and most of the other plugins use your markdown/yaml files as the source of truth and do not store side information.
If you are concerned about the additions or the workflows enabled by the plugins, just don’t use them.