I don't believe that a server should make me conform my code to it. The server should conform to my code through configuration files.
Also, if I am using a shared PHP head with relative paths my program requires additional programming logic to make the paths work. A css file located in /css/ is linked differently from /page/ and /page/subpage/ with relative paths, while it is always the same with absolute paths.
from /page/
css = ../css/style.css
from /page/subpage
css = ../../css/style.css
This is the same for images, videos, anchor tags, javascript and any other asset you could load, several of which are linked through a single head file.