I'm not sure it's "good practice" but it's the advised way of doing it by people that know a lot (http://www.howtoforge.com/forums/sho...82&postcount=4
I think it's to do with a quirk in how ISPConfig synchronizes/updates the vhosts files.
I THINK it effectively has a vhosts template which has things such as root, index, directives to get php working etc. When synchronizing, ISPConfig basically just adds the directives from the options field into the template without actually changing the template. If you look at the thread I link to in the first paragraph here, when I didn't put the "root" directive in a location container, there were complaints because there were 2 root directives at the same level suggesting it was just appending the root directive to the template, rather than updating bits within the template.
This maybe wrong, or a gross over-simplification but that seems to be how it works. I'm sure someone will correct me