If you use a hosting service, you will not be able to modify some of the branding.
If you host it yourself, you'll have some ways of modifying the branding.
You could for example, modify the home page so that it doesn't list the databases and put your user right to the login pop up.
You could also modify the dialog boxes that appear when you're accessing the website to remove the "FileMaker Server" text.
Do yourself a favor and just go back to FileMaker Server 12 until FileMaker fixes the huge problem with WebDirect.