I'd leave this one outside of the bullet list, as it applies to the last two points equally.

This should be shuffled way up higher IMO, probably close to the /rooted_ignore_pattern bullet point. Then the closing note about prefix order stands correctly after the list, but still directly related to the prefixes.

This first sentence requires serious mental capacity to parse, even for me as an advanced user. Better to split it into smaller statements:

"Syncthing will sometimes look at the files even inside ignored directories. Some file that matches any negated pattern (thus, should be included) could very well reside somewhere below them. This happens only for directories matching an ignore pattern after the first negated pattern."

Then the example, with speaking directory names that directly show what happens:

/1-not_looked_at
/2-also_completely_disregarded
!3-filename_to_sync_anyway
!4-foo
/5-could_have_foo_below_so_scan_it
*

Not that this is the ideal solution, but hopefully easier to grasp. So I hope you don't mind me just sketching the concept without following through.

Also a difficult sentence, should be split up at the comma and refactored. Speaking names in the example will help to reference easily. Include a number to avoid repeating long names here.

So far "this behavior" (U.S. English seems to be used mostly in the docs) is not very well understood, which makes it hard to see what exactly top-level rooted patterns really do. They're obviously negated, but don't cause something which essentially meant not doing something. So do they do it or don't they? 🤯

And "top-level rooted patterns" is a bit too terse for parsing correctly IMO, even with the example. The example is also negated btw. so does the remark apply to all top-level rooted negated patterns or what?

Despite having seen (but not thoroughly checked) the related PR, this special case suprised me. I.e. could be better explained.

A note about the version where this optimized behavior was introduced would help. Yes, we do have the docs versioning, but an unsuspecting user might not come up with the idea that the handling was ever different.