i couldn't find anything to back up either one except the bit about not being able to target flyers.
It's all in the wording, from pg. 84 under Hard To Hit:
Template and Blast weapons, and any other attacks that do not roll to hit, cannot hit Zooming Fliers.
Any template that is placed over a Zooming Flier does not hit it. There would have to be a specific notation for such an event in either the Blast or Template sections, which there is not.
As a side comment, I've seen templates used very wrongly with regard to hitting a second unit. Not saying that the guys you saw were misusing it but the rules for a template weapon state that we place the template so that it covers "as many models in the target unit as possible" and this stops you from angling it so it hits the main target less effectively in order to hit a second unit. Conversely if you've placed the template so that it's covering as many modes in the target unit as it can and it's also hitting more enemy models, they too are hit (unless of course they are a Zooming Flier, which is specifically excluded from being hit by template weapons in its rule section).