You clearly haven't played many RenPy games. There isn't a single thing in the engine which can't be moved or styled to the devs preference. Most typically don't bother cause it's not worth it but a good example would be Ben X Slave Quest; 100% custom UI. Academy34 is another good example.
As for the project you're referring to it's the
Qqsp Player which they updated to support HTML5 which does include support for more modern formats but those formats depend on the base they used for the web interface. Even then it's still inferior. For example HTML5 only supports VP8 encoding for webm files which is about equal to h.264 so you might as well use an h.264 mp4, RenPy supports VP9 which is on par with h.265. HTML5 also only accepts 3 file formats for videos, none of which are the commonly used mkv file while RenPy does.
Not really, HTML is only easier than Python, especially when working with a well written library like RenPy, in the sense that Python can be a little twitchy about spaces vs tab. Also to reiterate my above point. HTML5 supports 3 video formats with 1 codec each, same is true for audio. RenPy supports no less than 5 video formats with 6 different codecs options between them including ones more advanced than supported by HTML5, and 5 audio codecs. In terms of picture formats they're fairly comparable where the only advantage HTML has is animated gif support but you can achieve the same effect with more control and options in RenPy via code. HTML5 is also more problematic in other ways in regards to things such as volume control and offers absolutely zero security of any kind.