Just to backtrack a bit, the assertion that the price of customization didn't stop New Haven from ordering FL9's. The Alpert regime ordered the FL9s as part of a plan to phase out operation of electric locomotives (which they largely accomplished). The need to be able to operate the locomotives on third rail wasn't an option; if they wanted to run them in and out of Grand Central they had no choice. The new locomotives had to be dual mode. But the reason for choosing dual mode diesels was to save money by reducing electric operation. (Whether it actually accomplished that is very questionable but that's besides the point.) It wasn't an expensive add-on the New Haven wanted for its own sake, it was an expensive add-on the NH couldn't avoid.
Another factoid regarding the New Haven FL9s. I saw it written on the New Haven Historical & Technical Association message board, even the FL9s were ordered out of the catalog. They were developed by EMD in the late 1950s for Western roads, principally the Santa Fe, that used F units in long haul passenger service. (As we know none of the Western roads ever ordered them.) The 'L' stood for 'long.' They were stretched out F9s to allow for two water tanks for the steam generator. What's the source? One gentleman said it was reported in TRAINS Magazine news items at the time and other places (though he didn't mention what those other places were). That's not the greatest of references but there was a well known EMD veteran also posting in the thread and he took no exception to that. (He did object to some other comments.)
The F9 'long' unit design was modified for NH service of course. Instead of two water tanks the extra space was used for electrical gear for third rail use. The rear truck was modified as well with an idler axle in order to comply with the axle loading limits on New York Central's Park Avenue viaduct into Grand Central. But again, those were features the New Haven had to have if they wanted to operate the locomotives into Grand Central, not fancy bells and whistles they especially wanted. In fact the railroad gave serious study to instead converting the aging Alco DL109s for use on third rail into Grand Central. This would have been much cheaper but the Alco engines were just too heavy for the Park Avenue viaduct.