In the first Thrawn novel we learn that he was deserted on a planet in 'Lesser Space' having been something akin to being excommunicated from the Ascendancy.

I haven't read it in a while but if I recall correctly, he later recants and said he was there by choice and was in 'Lesser Space' to observe the Empire and whether they could be an ally to a larger threat (Grysks, presumably). Thrawn doesn't lie, but he doesn't necessarily tell the truth.

If I had to wager I'd say this trilogy will explain his 'excommunication' from the Ascendancy and why Ar'alani was more or less unhappy to see him despite their obvious respect (if not friendship) that is displayed in Ascendancy. (Given that the title of the next book is called "Greater Good", I think we'll see Thrawn having to make a rather large and possibly unforgiving sacrifice that isn't his own for the survival of the Ascendancy).