There is a note in the E350/E450 stripped chassis warranty guide (on the Axis/Vegas units) that says Ford should be on the hook for the alignment for the first year of ownership. I don't have a copy of it handy but several people have copy & pasted the text a few times on here.
Personally I just paid for the alignment at a local
Goodyear truck shop. It was something like $120 or so (mostly because this was before I knew about the Ford note).