In other words, could I purchase a 1 litre Trangia fuel bottle and the MSR Dragonfly liquid-fuel camp stove and use them together? Or would the smaller, slightly more expensive MSR fuel bottle be the only option with the stove?
The issue with the bottles isn't so much the "bottle" as it is the pump. On an MSR bottle, a pump screws into the top, then a specific MSR-style hose (from a stove) attaches to the pump. On a Trangia, the attachment system is different (as per This Gas Burner, or This One, depending on fuel, I think). The question in your case would be whether the threading is identical in the top of a Trangia valve as it is on an MSR fuel pump.
Based on this forum topic discussion on fuel caps (they were not discussing pumps, but the fitment should be similar or the same), I'd say that they are the same (and might be the same as Sigg and Primus as well). I don't own a Trangia bottle so I can't confirm this, but that's what the web discussion seems to indicate. Also, pages such This one, and This one indicate that there is a great deal of adaptability with such attachments.
I do have a couple of unanswered concerns, such as what pressure the Trangia bottle can withstand, and how adaquate the pump seal would be. Otherwise, I think it's worth a shot. Perhaps someone who owns both items can demo it and let us know.
As an amusing side note, even without any answers this question pops up on the first page of a Google search for "MSR stove Trangia bottle".
I believe the threads are generally compatible, BUT that's not the issue. Trangia bottles are not metal (they're a plastic like material, perhaps floridated HDPE). Trangia bottles are NOT built to handle pressure and could be very dangerous if used with a pressurized white gas stove (such as a Whisperlite, Nova, Omnifuel, Dragonfly, etc).
On the other hand MSR bottles are aluminum. Aluminum can be corroded by alcohol. I've read reports of aluminum bottles being "eaten" by alcohol.
In short, I would not interchange the two brands.
Although the threads may be similar (and even look the same) I've found that often the gaskets are not the same between bottles: flat gaskets, round, beveled and there is a corresponding difference in the rims of bottles: flat, round, beveled. Threads also tend to start in different places, and can have more or less bite/edge to them that can shred or deform the plastic threads on the pumps.
Having suffered enough leaks (and fires) by mix-mashing bottles and pumps (often without being able to identify why - gaskets were good etc.), I've adopted a policy of only using original bottles with pumps. This also is fairly standard among the professional outdoor guiding companies I'm familiar with.
Good practice: Use the original bottle to attach to the stove, and carry your extra fuel in another bottle with its own original cap, and refill the stove bottle as needed.
I first bought a MSR Fuel Bottle (325 ml, aluminum) for packing denatured alcohol for my Trangia stove. Hiked with it for over a year with no leaks (safety-lock cap) or issues. Just bought a Trangia Fuel Bottle (300 ml, polythene) with push-button cap for dispensing fuel. Both high quality bottles. Discovered that the caps for each bottle thread into the other product bottle, no problem. Though the O-rings and cap lip are slightly different sizes, the Trangia dispensing cap easily threads and seals into the MSR bottle. The MSR safety-lock cap does thread into the Trangia bottle, however, the safety-lock cap does not completely seal on the Trangia bottle due to the (larger) metal reinforcing ring on the Trangia bottle preventing the cap from fully seating. I also tried the MSR Expedition Fuel Bottle Cap (non-safety cap) and that sealed on the Trangia bottle, but the cap lip and O-ring size were slightly larger than those of the original Trangia dispensing cap. I have not field tested the Trangia dispensing cap on the MSR bottle, but in a 15-minute inverted position leak-test there were no signs of fuel leakage from the thread/cap area. The Warning on the Trangia bottle warns "Don't pressurize the bottle." The MSR bottle advises "Contents under pressure."