From a collectors point of view I'd lean heavily towards the Commodore one. 20 years down the road, someone that's getting nostalgic would probably prefer the Commodore one, not just for the name, but because (even if it isn't entirely true) it would seem to have no compatibility issues.
Were I to get an Atari 2600 now, I'd want the very original, not one of those they tried to resurrect in the mid-80s for a cheap price. The value difference is minimal (having a quick look on ebay, the all black 4 switch is about $10, wood grain 4 switch $15, wood grain 6 switch (earliest) is $20) but that's the idea. It's also the case that systems generally aren't as valuable as rare games (speaking in old console terms anyway).
But production run does figure in, too. If there were very few non-Commodore ones, the value might increase. But you're looking at demand overall. Non-collectors (someone that has some cash burning a hole in their pocket and thinks "Man I used to love to play games on the Amiga") or casual collectors will want just one Amiga, and would aim for a Commodore. But a serious collector would want both for completeness and if there are few AT machines out there, the value would be high. If there's a bunch, probably little to no demand.
From the standpoint of 'which is better' then you might figure in 3.1, the floppy, reliability and age, stuff like that. But that only figures in from a collector's point of view if it changes demand somehow.