When not to contact a professor for a PhD based on what is written on his web page?
I assume the note on the web page is to avoid misunderstandings about the application process. In some places (not the US generally) it is the professor in charge of admissions and he/she actually hires students for the lab. If students from around the world expect that to be the case, the professor may have to deal with too many individual situations, so just makes a general statement. 

It isn't, I suspect, a statement that you should not contact him/her, but a warning that you need to go through the administrative admission procedures first before you can be considered. 

You can contact the prof for information or to express interest, of course, but be clear that you are also making a formal application through proper channels. 

The contact isn't necessary, however. There will be time for that after you are accepted to the program.