BTW: Here you could use PIWIK_INCLUDE_PATH . CustomLogo::getPathUserLogo() and same below

I copied the code from the existing hasSvgLogo and getPathToLogo methods for consistency :). Is there any difference between the static method and the constant? Should I still use the constant?

good point, I didn't notice that. Consistency is always good. We usually always use PIWIK_INCLUDE_PATH but not sure why Filesystem::getPathToPiwikRoot() was used there is there's no difference and the constant should be better. I'm ok with Filesystem::getPathToPiwikRoot() in this case. To remove the duplicated code though maybe there could be a method like

private function getRootPath()
{
    return Filesystem::getPathToPiwikRoot() . '/';
}
// or 
private function getAbsolutePath($reference)
{
    return Filesystem::getPathToPiwikRoot() . '/' . $reference;
}

As you prefer, we can also replace all calls to this method in this file by the constant.
If we add a new method getAbsolutePath, I think it should be in the Filesystem class, isn't it ?

Somehow I would prefer not to have it in Filesystem but would be also ok there. Having a look at this again in the code there is often file_exists($pathToPiwikRoot . '/' . $customLogo) etc, finding several file_exists. The code seems quite confusing in there in general and needs to be refactored at some point. Maybe there could me instead a method

private function logoExists($reference)
{
    return file_exists(Filesystem::getPathToPiwikRoot() . '/' . $reference);
}

Of course this could be as well in Filesystem but might be as well fine in CustomLogo for now

Done in 637b839 ;)