Currently kompozer will ignore php files if they do not have html/head/body tags. I have read the same problem arises for .tpl and .asp files. A quick way to circumvent that would be to add the option to edit those files in a text only mode or in an external editor. The best option would be to add this in the preferences (edit this file always with this editor or add a group of external editors that can be selected by rightclicking)
Same goes for images / flash / xml etc.
One of the reasons to use a program like Kompozer is as a way to organize your sites - and edit the html portions of that site - and this feature would make it more usable in that respect. Kompozer can never be an all in one package because it will never be the big image editor, for instance.