Because Aragen is only concerned with knowledge, he is neutral to most. However, most deities are not neutral toward him.
Right but most isn't all and which ones he's not neutral to should be known.
While Trickery/Travel is a forbidden combination, for Aragenites it is not an issue since Knowledge is a required domain, thus eliminating the possibility of Trickery and Travel together.
I think you may be confusing some deities, as Aragen has Knowledge, Travel and Protection as domains. Trickery/Travel is therefore never an option as Trickery is not one of his domains.