No. It does not overwrite anything nor does it make anything invisible. The only thing the codepoints you're referring to can do is make things appear out of order (and that's a bug in editors for not rendering them as special characters, not a bug in Unicode). There are invisible codepoints (such as ZWSP) but they also have are also necessary and again, a failure to render them as special characters is an editor bug. And they don't make anything else invisible.
(* There have also been other editor/renderer bugs such which might result in crashes or disappearing text, but those are from failures to be compatible with Unicode, not from Unicode)
You need to go read the paper I linked (which is linked from your blog post), not a 3 paragraph blog post.
If you think that these are errors in Unicode, then I have some errors in ASCII and a text editor that treats NUL as end-of-file to sell you. Control characters have always been necessary and will always be necessary.
> eurt ton
I'm not even going to address that other than to say LOL