As stipulated in the Dev Log, the Commander gave up the chase because of his responsibilities.
He tried to get back to his tent because of his responsabilities, but it was not the reason he fled. At least this is what is written in the devlog. I'm asking why he fled in the first place.
I have a question: How can the sneaking apply to fort mode exactly? You don't control anyone dorf, and it seems like we're no were near getting the Bloat of controlling one Dorf during Sieges, a la adventure move. A lot of the sneaking stuff, is conveying information to the Player so there no translation for that stuff in Fort Mode.
The new mechanics can be applied to fortress mode even if the player doesn't have direct control (field of vision, raising alarms, and so on) and may impact gameplay regardless of player control. Or it may be the the same as it always was. This is what I hope Toady answers.
If you have a lot of this kind of doubts, you aren't being helpful trying to answer the questions for Toady.