Even the sandbagged number for the GCP subway extension was $2.7B, not including any intermediate stations:
http://ricondoprojects.com/LGAAccess...s_20200817.pdf
(page 2-55)
The reason given for killing it was construction impacts to Amtrak's Hell Gate Line (lazy argument, this is really no different than any other bridge replacement on the NEC) and the reduction in service to Astoria Blvd and Ditmars stations as a result of the branching, which is a decent argument.
However, I think the new branch could be constructed with a 2nd set of platforms at Astoria Blvd alongside the existing ones, which softens the blow to existing service quite a bit.