Well, a method of doing custom CSS would be nice... but only for certain
values perhaps 

* Heading fonts
* Link colors
* Background color

Otherwise there is the risk of making the person doing the customization
have to do A LOT of CSS work that is likely to break when Loomio is 
upgraded.

But in regards to the method you mention- that was just for uploading a
custom logo, not CSS at all. Unless you've the logo to be invoked via
CSS instead of an <img> tag, it doesn't seem that CSS would solve the
issue?