making any bottle into either a "sippy" bottle (smaller 16-24oz bottoles typically mounted AR-style on one's pack straps) or a hydration system (1.8L to 2L bottles typically) is really not very difficult.
even a klutz like me can fabricate one.
here are three suggestions for doing so. i've done the first two, and one long time Forum participant swears by the third, though my first thought was the same as your observation, viz. "How does that work again???" (since the bottle is semi-rigid and doesn't collapse, thus drawing a vacuum which "fights" water flow).
1. buy a hydration conversion kit containing various size caps for many, many popular bottles (1L Lexan, Gatorade, various poplular smaller Spring Water & Soda Pop bottles), hydration tube and bite valve. The caps are vented with a self-sealing vent so leaking when the bottle isn't upright does NOT occur. Sorry, i don't remember where i purchased mine (Brigade Quartermaster's, maybe??? - i'm thinkin' on it and will clearly edit this post if i figure it out - it was a very nice, relatively inexpensive kit).
2. get some hydration tubing sold separately on this website originally intended for Platys (Anyone, is that spelled "Platties" in Oz?) and...
bore/drill a hole the size of the hydration tube in the original bottle cap. Sometime i wrap some duct tape around the tube where it will mate to the bottle cap, so the hole needs to be a little larger. However, even when i don't do it, i smooth the bored/drilled hole edge and since there is little relative motion b/t the tube and cap, not much wear takes place. then,...
starting small, and if required, working up to successively larger holes to obtain desired flow for desired suction-effort, bore/drill a vent hole in the bottle cap (this takes care of the issue you were envisioning of a non-collapsible, semi-rigid plastic bottle). A small piece of duct tape is used to cover the vent hole and prevent leakage when the pack is stowed in my bivy at night. And, yes...
i use a 1.8L Spring Water bottle in my Hunter's Lumbar Pack - it has a water bottle pocket that i can just fit the 1.8L bottle into by inserting while twisting/screwing the bottle into the pocket - that sucka' ain't ever fallin' out - biner or no!). A 2L bottle has just slightly too large a diameter for this water bottle pocket which was originally intended for 24oz SportTop bottles (it came with one) and has a cord-locked bungee at the top of the pocket to secure smaller bottles (unecessary w/the 1.8L bottle).
i've tried it a lot and this works fine. Sure the bottle is upright and i have to draw the water up, but this really isn't that difficult, IMHO, even after a steep ascent and HR is up and breathing is consciously being controlled.
3. the long time Forum participate i mentioned earlier uses an inverted rigid plastic bottle with a leak-proof cap. he claims that he just sucks (THIS IS NOT meant as a double entendre!) and draws a bit of a vacuum until the semi-rigid bottle starts to collapse. i've never tried this, but i would imagine that the water in the tube is probably sucked back into the bottle when he no longer is drawing water from the bottle (unless the bottle deforms and remains mostly in that deformed state). BTW, this might be nice for below freezing weather if it really did automagically draw the water in the tube back into the bottle. Furthermore, wouldn't it be a simple matter to also just bite on the valve to keep it open for a brief time after drinking so that some air is drawn in also? This would prevent a cumulative build up of negative pressure as more and more water is drawn from the semi-rigid bottle.
Anyways, again, i've never tried #3, but he swears by it. In my case, the bottles are stowed and used upright and vented to prevent collapse or a vaccum from being drawn.
Main downside to spring water and soda pop bottles is filling them. Two issues: small opening and shallow water sources. Using a bandana as a pre-filter, in deep water it's not too difficult, but takes a while due to the small opening which is further impeded by the bandana pre-filter. In shallower water, the bottle is manually crushed to some degree and then filled as much as is possible. My 450-600 ml Ti dual-use heating/drinking cup can be used to scoop water and pour through the bandana pre-filter which i've placed over a small lightweight funnel to facilitate fillng the water bottle by pouring when water is too shallow to finish filling the bottle (the funnel is one of those small alcohol/fuel funnels in a different color fr/my fuel funnel and also clearly marked with a 'Sharpie' water-proof marker in two locations on the funnel; the funnel also has a mesh filter, but i don't know the pore size). If i use my Ti cup for scooping water, I don't use the Ti cup again w/o heating the water to make sure any little bugger on it which is still viable is killed. Generally, i don't use my cup in this fashion however.
Best way to fill small mouth plastic bottles, IMHO, is either a pump filter or a gravity filter.
Perhaps this is too much detail and probably more than an experienced L/UL-er like yourself requires? Hopefully, the verbosity will prove helpful to any 'newbie'. If i failed to answer your question, or muddied the waters, so to speak, w/my extraneous verbosity, if you are daring enough for a second dose of verbiage, just post back and i'll attempt a clearer, more succinct reply.
Still searching for source for the conversion kit. REI sells one to convert an inverted Nalgene Cantene into a hydration system. REI also sells a "sippy" kit to convert an upright Nalgene Cantene into a "sippy" bottle.