I too use a Maxped bottle holder to hold my nalgene, cup, and other items.  To increase the space, I trimmed out the insulation and inner layer of fabric.  I now can squeeze in a Trangia burner and a fuel container. 
Thanks, I should have also mentioned that.  I carefully cut out the insulation, too.  That made enough room that I can fit a bain marie pot in there.  That's an insert made for commercial steam table/wells in a restaurant.  They're heavy gauge SS and have a lid, and I found a 1 L one that nests nicely with my 40 oz bottle.  Not as light as a $50 titanium pot much it only cost about $4 with lid at a restaurant supply store.
Thanks to to the OP for the original post.  I don't mean to hijack it; it's a very good idea.  Your first post gave me a few ideas to tweak my own kit.  I should take a few pics of the contents of mine.  Mine is also biased heavily towards fire.
Using the bottle holder does as some bulk but it also provides a means of carry.  It has a should strap, plus it has a bunch of MOLLE webbing to either mount it to a pack or lash it to a vehicle.  Lots of options.
At any rate, I personally don't like to carry an empty water bottle.  You save the weight of the water but none of the space; plus, I would rather have the water!  Of course if I lived in MN instead of SD I probably wouldn't carry water, just the container.  It all depends on your environment.