I have no DIRECT evidence as to how GM&O got permission to get a DL-109 in February 1943, but....
The GM&O's Dl-105 and Dl-109 units had the same 80mph gearing as the New Haven's (and-- cf the "Dl-109 Traction Motors" string for evidence and references-- PROBABLY the same, relatively heavy-duty, 726 traction motors). (All other Dl-100-series locomotives were apparently BUILT with 120mph gearing and 730 traction motors, though some were regeared and may have been remotored later.) From its construction number (69991) and Works order (S-1866-12), it looks as if it was built as an add-on to the New Haven's second order (cn. 69980-69889, w.o. s-1866-1/10), delivered between 7.42 and 1.43.*
The New Haven's units were classified as dual-service. The GM&O's units would seem to have been physically as capable of dual-service application as the New Haven's. So my SPECULATYIVE GUESS is that "it's really for dual service" may have been part of the GM&O's sob story to the War Production Board.
* Anomaly: the Southern's unit DP2904 -- despite having been built earlier (shipping date 6.42) and having the high-speed gear ratio -- is also in this block: c.n. 69990, w.o. S-1866-11. Your guess is as good as mine.