Is there any way of changing the standard by which NetBeans automatically formats the code when doing "Source->Format"? I seem to remember seeing this option somewhere, but I can't find anything about it.
You can change a very limited number of settings related to formatting.
open up netbeans IDE
Go to tools->options
click on Editor button on top left of the options dialog box
click on the formatting tab
select PHP from the language select box
then you would be able to see the required settings that can be changed.
Latest version 7.3 will solve most of your needs.