Why can TinkerTool change the font of the Finder, the Dock, or the menu bar?
The Finder, the Dock, and the menu bar are mainly using a Carbon-based user interface. Carbon emulates the legacy technologies of the classic Mac OS which did not have a feature allowing users to change their font preferences. For this reason these components will ignore font settings. You can use applications that take advantage of the old “theme” technology to modify the look of Carbon applications. Note that most of those applications are not really compatible with Mac OS X. They basically destroy the graphics resources for the operating system and replace them with their own versions. The changes are applied to the whole system, not one particular user, and sometimes the modifications don’t survive system updates.