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You mean one theme for books and another one for comics ?

If so, you can already do that by creating your own theme: the theme used for books is defined in the "books.css" file and the one for comcis in the "comics.css" file.
Unfortunately, mass download is something that has to be managed on client side (in your case by the Chunky app). The server alone cannot provide bulk download.

To hide the navigation you have to either:
  • press "Enter", if you have a keyboard
  • tap/click in the center/bottom area (the empty one)
Let me know if you still can't exit the navigation interface, as this might be a bug.

Thanks for your donation. :)
Once a file has been scanned, it is not scanned again unless it has been modified or renammed. So the extra step of guessing the correct file type is done only once by incorrect file.
However, it happens once for each page when reading a comics using the online reader, so it's better to have correctly named files from the beginning (although the guessing step is very very fast).

I will not add a renaming feature to Ubooquity as it would go agains one of its core principles: "do not modify the files of the user", ever. But I have found a small tool that does just that: correcting the extension of CBR/CBZ files (it has a few other useful maintenance related features and is really simple, so it's worth a look).

The tool is ZenCBR.