According to the Sublime Unofficial Docs, packages (including any key bindings) are loaded in the following order:
Packages/Default;
- shipped packages in lexicographical order;
- installed packages in lexicographical order;
- all remaining user packages, except for
Packages/User, that did not override anything, in lexicographical order;
Packages/User
Basically, any settings you have in Packages/User are the final word in what happens. So, if an installed plugin tries to use a keybinding for which you already have a definition in Packages/User, it won't work – your settings will override it.