(I am the website author & tech co-creator with Said Achmiz.)

> Everything is in black with white borders so the layers of pop over is hard to distinguish from everything else.

They have double-white borders and drop shadows. It looks reasonably distinguished to me, but I suppose we could try one of the very light grays to see if that helps.

> The close button is also only at the top which isn't immediately obvious to find when you've read the text and is hard to reach on big mobile screens.

...Where else would the 'X' close button be?

> it's also in black with white borders and looks visually more part of the page then the pop over

The 'X' is right next to the title, it definitely does not look like it's 'more part of the page than the pop over'.

> It also scrolls the back page to the link, so when you close the article now looks different then it did.

If it didn't do that, then the anchor & context for the pop-over wouldn't be visible or the pop-over would have to be absurdly small whenever the tapped-link wasn't at the top of the screen already. So the shifting-to-top is good.

I think you're right that it should restore the position. It was originally a pop-in, so that didn't come up before we recently swapped to pop-over.

> that uses the same anchor text and looks like it goes to the same place!

I'll modify the text to be clearer.

> now in a tiny size with a screenshot of even tiny text to add to the confusion. Just in case you can squint to read it's all made slightly transparent so you can still read the 4x larger original article text underneath.

That is not how it's supposed to look, and doesn't on other pages - just here. Amusingly, it's caused by an interaction between the .sidenote class, and the page URL being 'sidenote'. (Nor is this the first time! JS and web browsers, man.) If you had tried it on any other page, like the section links of the abstract in my most recent page, https://gwern.net/suzanne-delage , it would've been fine. We've pushed a fix.

> I commented then that that article had some wonderful "footnotes", they just expanded inline you could read or not the extra info very easily.

It's a good essay (https://tylervigen.com/the-mystery-of-the-bloomfield-bridge) but the footnotes are not the highlight of that page.

- The zebra-stripe blockquote styling is annoying and makes them hard to read with visual moire (but can be fixed).
- The fact that you have to opt into them with no indication of whether they are worth reading means cognitive burden (and while some are quite lengthy and worth reading, many are not). The author alleviates this a bit by sometimes specifying 'long note', but that increases the authoring burden, and doesn't solve the problem much (short notes can be interesting too).
- 'Note' for each anchor is verbose & repetitive.
- The footnotes are not aggregated at the end, so you can't skim or check them en masse. (And did you think you could just read or search the HTML source? Not without additional processing or word-wrap options to fix the ultra-long lines.)
- The lack of a real hover popup is made up for with the hack of using tooltips - an idea I tried and abandoned very early on, because it strips formatting & cannot be made interactive or accessible; in his case, his tooltips are actually worse than useless because they silently, without indication, strip out large parts. For example, one tooltip at least bails out and tells you to click on it to see the email he sent, so at least you know you're losing everything, but then a later one ("The feds would pay up to 90% of the costs") silently drops an entire chunk!
- The tooltips + default collapse also means that they aren't searchable: C-f 'pro-rata' will turn up nothing, because it's hidden in a footnote. (This is solved by aggregating or display by default; if one chooses not to do that, one should do something - for example, detect the search event, uncollapse all of them to make them visible for search, and then recollapse.)

I can't fault it on some issues like mobile handling or multiple+large footnote handling, but that's only because it avoids the problem of desktop sidenotes entirely, and is just the mobile version. (Which is why I didn't bother to link it: it doesn't do anything better than the examples already on the page, although now that I've looked closer, it may be worth linking as an example of the problems with trying to stuff footnotes or annotations into tooltips.) You like it because you don't want desktop footnotes at all, apparently, not because it represents a good solution.