You bring up a valid point.  I am no expert, but I simply do what I can to prevent spending my precious camping time being sick.  Some roll the dice and don't filter at all as that has worked for them. 

For me it is just a matter of convenience.  I start my trip with a clean filter, so when my filter clogs I have clean water readily available.  My DIY filter is setup around camp and not down by the water, so it's more convenient to just grab a cup, pour some clean water and fill the syringe right there and perform the backflush.