I’m aware that the character Jose Chung appears in one episode in both series but does that even count as a crossover?
Sure, I don't see why not, especially since he was a memorable guest star in both. Add that to Frank Black's appearance in an X-Files
episode, and I think that pretty much states that the two shows are definitely set in the same universe.
Except for that one episode of Millennium
where they were watching The X-Files
character cameos like in Soul Calibur don't count. Darth Maul and Wolverine both appear as unlockable characters in Tony Hawk's Pro Skater 3. that doesn't mean they co-exist.
Apparently you missed that deleted scene in Episode One
, where Maul challenges Obi-Wan to a skating duel, but Obi calls Wolverine to sub in for him...