How have you customized official adventures for your campaign to justify acolytes of an Inquisitorial Ordo other than the threat of that adventure?

I haven't really needed to do it, because most of the time it doesn't matter what Ordos a few acolytes belong to, because they will inevitably stumble over threats and conspiracies that their Ordos usually don't deal with, but still have to figure out a way to pull through.

Only slightly or not at all. Even if an Inquisitor is a member of one ordo he is still interested in all threats to the Imperium and will dispatch Acolytes to deal with all sorts of threats. If something's amiss about Confessor Suspicious, you can bet that an Inquisitor would send men to investigate even if he's a member of the Ordo Xenos. I don't really think it's a problem. Inquisitor's have their fingers in a lot of pies.