You already answered yourself.
The order on trakt is the 'Aired Order' and that is for all series.
If you're using a MediaCenter that automatically scrobbles, then it shouldn't be an issue, if you're manually checking in then you will have to be careful which one you select.
Shout by DaveVIP 11BlockedParent2013-07-22T00:32:56Z
What the hell is the right viewing order? I've heard Netflix actually has it right for once, so that's what I'm following.. not the order from here.
via http://www.netflixfixer.com/2012/09/firefly-intended-order-and-by-airdate.html