Take for example that "Jump to" text box - if your native UI toolkit doesn't let you add icons into the placeholder text like that (does it even have placeholder text natively?), you'll have to deal with drawing offsets, caret position, or possibly nested components, overriding focus outline, in the worst case resizing the stuff when focused, and other stuff that makes the whole endeavor not worth it due to the added complexity (assuming that text box works how I think it works, I haven't used Slack in a while).
And I don’t think it’s quite as hard as you describe natively, at least on AppKit/UIKit, windows, and android.
It would still look mostly native (even though it's clearly not a native control), be very performant and use a tiny amount of memory.
Your examples of boring native UI is the result of developers that don’t bother to exploit these features for whatever reasons- probably because it can be extremely time consuming to build native custom UI and adds mental overhead unless one has/is a dedicated designer/artist.
I’m not sure which part of the Slack UI you believe can’t be done natively? Flat colors or the revealing menu?