I end up hunting a lot where water is severely limited so I almost always take more than one bladder. I always have the 3L big zip and supplement with non-zip bladders of whatever sizes I need. I try and minimize weight as much as possible but feel the zip is very worth it for ease of filling. I'm usually filling the bladder with my camp cup or cook pot from small seeps and springs and the zip makes that easier. I went a few years prior without the zip and was very glad when I made the change.
Granted I'm not running any inline filter I'm just using Aqua Mira for treatment so my use is slightly different from yours but still, for getting water from a source into your dirty bladder the zip makes life easier.