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.