The outbound flight and Jorus would be easy enough to explain in the canon timeline, but the clone wars being an army of Mandalorian clones attacking the republic? Maybe there were 2 clone wars that Kenobi fought in? I don't know how or if the EU tried making the history in the Thrawn Trilogy fit or if they just kind of ignored the background that did not fit with the "new" canon from the prequels.
It really had no direct effect on Thrawn himself, just the trilogy and it's cloning storyline drew on a completely different 'clone wars' than what became canon.