I think this happens in most distros if not all. Not sure why though and if it's fixable.

Hi and welcome! It would help if you tell us which version of Ubuntu Touch you are running. When search for updates, what is the selected channel? There are a lot of things landing on the PinePhone right now so maybe Release Candidate or even devel would suit you better if you want the last changes even if still unstable? About your keyboard, you can turn it black in the settings, in "Language and text" you have a keyboard theme. "Just black" is awesome. You can also activate the Suru Dark theme with UT Tweak Tool as said above.