I think the main problem with Trell being autonomy comes from characterization present in BoM. Based on what we see in the book, the faction values logic, order, and controlling the world around them to an almost obsessive degree. In this, they are hypocritical; they chafe at their limitations, but want to control everyone else. Furthermore, the agent of Trell who confronts Suit dispassionately discloses that they are changing their plans to exterminating life on Scadrial because they are growing too difficult to predict and control- this in particular seems contrary to the idea of Autonomy. For that matter, it doesn't feel very much like Odium either- if anything, Dominion (though he is dead) is the closest fit of known shards in my opinion. Even the names used in their cult stinks of an obsession of making sure everything is accounted for and controlled- set, suit, series, sequence, array, etc. Additionally this is thematically opposite to Harmony's hands-off approach to parenting Scadrial which has been getting a lot of attention in the story; these guys are the other extreme, meddling in and trying to micromanage everything.
Pretty much all of their members have strong rejections of the idea of some things being out of their control. Suit, for example, goes into denial. Even when he is completely helpless and at the mercy of another, he tells himself he is finding an advantage, doing something productive. When Sequence reached the age where she understood her own mortality, she rejected the idea. The Array with the limp similarly was obsessed about avoiding death.
And Miles.... Miles seems broken. Like a postman snapping over the idea of a never ending burden, he looked for an alternative solution.
I'm not really sure at all what Trell is... but my best guesses are a shard we haven't seen, some kind of rogue embodiment of a piece of Harmony, or a whoopsie-daisy collateral effect of something Kelsier and Lestibourne did.