If you want to add a new category (site type) to a tool, you have to change all the /tools/toolid.xml files. You could have all those files in sakai.home rather than distributed across webapps, but you still have to change a lot of files, and also, in the long term, you could be affected if changes are made to the original files since you are using now a modified copy of them. We think that most people just modify those files for adding new categories but those files include other things like tool title, function require...
Therefore, It would be good to have them work independently. If you'll be able to add a property like tool.categories.toolid=category1,category2,category3,.... you could manage all tool categories within the same file, avoiding the copy of the entire toolId.xml file.