Yes, it's top-heavy if trying to stand up an empty bottle. I'll just put the little cap back on the mini and lay it down if I don't just filter it into the other bottle first. I guess it would depend on the specifics of a pack if it would be a problem carrying it empty that way. I'm setting it up in a Murmur and between deep enough pockets and shock cord side compressions holding it against the pack, it's not an issue.
I'm not a "sipper" though, nor am I agile enough to reach back into a side pocket. I tend to tank up more than sip while I go, so getting the bottle untangled from the compression cord isn't such a big deal that way. I've never found a way to use a bladder/inline filter/hoser that I was happy with.
Something I kind of want to experiment with though, is leaving the mini loose a quarter turn. There would still be a full turn of threads holding it on the bottle, but it would leak air. Then attaching either the supplied straw, or a longer piece of tubing, down into the bottle, I could attach a hose to the outflow, and possibly a bite valve and use it like a hoser then.
---Edit: I just did a little playing around with a couple hoses on this idea and I gotta say, I think I might be a hoser convert. Don't even need a quarter turn loose, anything short of locked-on-tight will do. Sure it may dribble a couple drops when it's filled to the brim and you sling on the pack, but no biggie. To fill the bottle, I didn't even need to unthread the hose from the pack, or take the filter out of the straps/cords. Just unscrew the round bottle and slip it out from under the filter and draw-hose.
A large reason why I'm incorporating the mini attached to the bottle, is for storage. I feel better having it there than just stuffed into a side pocket or mesh back, or opening my pack and digging it out of a baggie when I get water. Again, it comes down to the "system" philosophy. This way works with my pack "system" that has no hip pockets and limited storage. Just seems like a good fit for me.
I like the sink idea. I also love how these systems are so expandable. Headed to a dry area? Pack along a 2L bladder. Extended camping? Bring 2 bladders, hook up a gravity drip with a hose. Be creative :)