Customise general webmail options through WHM and/or cPanel

While there are many ways to customise the likes of Roundcube, Horde and SquirrelMail through the command line - it's a somewhat convoluted process and means having to maintain a whole bunch of stuff every time cPanel rolls out an update.

It'd be nice to be able to customise common aspects of each webmail system through a WHM (or possibly, for customers, cPanel) form. For example, I'd like to adjust the default fixed-width font for Roundcube so that it's slightly larger. Or I might want to use my own logo.