The minimap is, in fact, the best idea anyone has given me today (and I think it addresses a concern 3 other people brought up in this thread). The underlying problem with all the suggestions is that you lose all the scaffolding, the paragraph breaks, the line spacing, the sense of where you are in the text that makes it easy to just jump into the text anywhere in the first place. I think this peripheral low fidelity map addresses it because you don't have to actively engage with it. Your concern about the control to not draw attention from the text is the entire point of this design. You can't make it too salient because that makes it steal the focus from the main text, which defeats the entire point.

I already have the info on paragraph and chapter breaks in the reader already, so this is more of a rendering issue rather than info display. The reason why I particularly like your first suggestion is that it lets you know something like a poem or different paragraph style is about to start so you can change your reading pattern accordingly rather than stumbling into it when you're already in prose mode reading at 400 wpm.

On the 2 modes thing, I feel like there isn't really a good reason to do it the other way. It was more that it happened that way rather than it needed to happen that way, and you're right that the main one should probably scroll and have bookmarks rather than making the user make a choice between 2 different interfaces.

Theme circles is definitely a solid suggestion, being a more practical implementation of visualising the underlying theme. Being able to see the actual colours of the background/text rather than an abstract blob is good, so that's a definite maybe.

Code isn't public yet, but extensions are something I've wanted to try for a while. In fact, someone sent me an email this morning asking precisely for that, to be able to paste a link and read articles. It can't be done directly in the page because of CORS policies, and doing it server side would involve routing the reading of articles through my server which is probably not ideal for everyone. An extension that pulls the article from whatever page you're on would be the most ideal version of this, from a privacy standpoint, so I'm considering it.

And finally, your last point is actually the first pushback I've had all day on the controls/interface. As far as 4 other people having difficulty finding the thing, I think you're right that something needs to be done, but I don't think hiding the options behind discovery is really the answer. There is a conflation in my brain between 'controlls are easily found and accessible' and 'controls are not hidden beneath layers of menus/bookmarks', and I think it's a false conflation, I had been treating them as one. Thanks for that.