The template filter isn't aware of what context it is in, which can cause some significant issues with filename conflicts.
Extension 1 has a file named styles/prosilver/template/header.html
Extension 2 has a file with the same name.
Extension 2 tries to include its header.html file, either on its own page or, for example, on template event overall_header_head_append.
(<!-- INCLUDE header.html -->)
The styles/prosilver/template/header.html from Extension 1 will be included since its name comes first (the include calls locator->get_first_file_location() to try and load the first location the file is found at).
This affects everything that can be included in template files--other template files, js files, php files, and css files (once that is implemented).