It seems to me that the trademark policy is not all that different from section 2a of the GPL; if you do make changes, you have to take responsibility for those changes, and it's a logical extension to the case where some of the recipients don't read all of the source files.
Regardless of the legal mechanism, it makes sense to ask who is supposed to be responsible for the pre-installed web browser executables on Linux systems. If Fedora is accepting bug reports and fixing them, they're taking the direct responsibility, and so these executables should be branded in such a way as to let users know this. If the user has downloaded the browser directly from Mozilla, or the distro is just redistributing Mozilla's download, it should be Mozilla-branded.
Of course, most packages don't need a distro branding, but that's because most packages don't have a big user-facing project. Kernel.org, for example, doesn't distribute and maintain built Linux kernel executables that end users are expected to download and start using because they saw a Linux ad in the newspaper.