I agree, it kinda sucks, but the provision was only ever intended to give captain upgrades their ATP all in one checkride; not give an employee their ATP without upgrading. . .

§ 61.39 Prerequisites for practical tests.

(b) Notwithstanding the provisions of paragraphs (a)(1) and (2) of this section, an applicant for an airline transport pilot certificate or an additional rating to an airline transport certificate may take the practical test for that certificate or rating with an expired knowledge test report, provided that the applicant:

(1) Is employed as a flight crewmember by a certificate holder under part 121, 125, or 135 of this chapter at the time of the practical test and has satisfactorily accomplished that operator's approved—

(i) Pilot in command aircraft qualification training program that is appropriate to the certificate and rating sought; and

(ii) Qualification training requirements appropriate to the certificate and rating sought

I don't think anyone imagined FO's being required to have ATP's when this reg was written, so I wouldn't be surprised if this reg is re-written in the future. Kind of a tough break for now though . . .