If I'm reading the law correctly, they don't have to submit anything to AASHTO:
A State having jurisdiction over any segment of routes and/or corridors referred to in subsections (c)(18) shall erect signs identifying such segment that is consistent with the criteria set forth in subsections (e)(5)(A)(i) and (e)(5)(A)(ii) as Interstate Route 69.
(A) IN GENERAL- The portions of the routes referred to in clauses (i), (ii), and (iii) of subsection (c)(5)(B), in subsection (c)(9), and in subsections (c)(18) and (c)(20) that are not a part of the Interstate System are designated as future parts of the Interstate System. Any segment of such routes shall become a part of the Interstate System at such time as the Secretary determines that the segment--
(i) meets the Interstate System design standards approved by the Secretary under section 109(b) of title 23, United States Code; and
(ii) connects to an existing Interstate System segment.
(c)(18) is the entirety of I-69 except US 59 southwest of Victoria. It also includes "from Sarnia, Ontario, Canada, southwesterly along Interstate Route 94 to the Ambassador Bridge interchange in Detroit, Michigan" and "from Windsor, Ontario, Canada, through Detroit, Michigan, westerly along Interstate Route 94 to Chicago, Illinois". So Michigan and Illinois are probably breaking Federal law by not posting I-69 signs on those portions of I-94 east of Chicago that are up to Interstate standards 
GREAT observation. A couple of months ago, I took the liberty of running your observation by FHWA (I had always thought, probably mistakenly, that the mandatory signage applied to I-66 and I-69 in Kentucky). I was advised by phone today that it is currently under review by their legal counsel.
As an aside, I have had great difficulty in finding a current, fully amended, version of Section 1105(e). Interestingly, the individual at FHWA told me that they have the same difficulty.
FHWA expects to give me their position on the mandatory signage in the near future. I will post as soon as I receive an answer.