Still and all, Thameslink connected a pair of lines to the northern suburbs to a pair in the southern suburbs with dual voltage MU trains. They also found an abandoned tunnel to facilitate it. Manhattan does not have that, Thameslink is not universal thru running, they didn't rip out stub terminal tracks using the RethinkNYC codeword "widen the platforms".
They also use RER, SEPTA, and MARC/VRE analogies. I don't know a thing about RER, but the latter two are invalid. But do understand their hidden agenda - they are neighborhood building preservationsists trying to save Block 780 and will grasp straws. They tried to get Penn Plaza 2 knocked down to replicate a new Old Penn Station (PP2 just got rebuilt), tried to save Hotel Pennsylvania across 7th Avenue (torn down in 2023), and also making a fuss over the abandoned Pennsy power house as the last remant of old Penn Station on Block 780. (Nobody cares and there is another one in LIC converted to condos).
Throw in planner hyperbole of unifying the region by abolishing that transfer (can be done in 2 minutes) , cut traffic congestion, address climate change, all hypotheses they can't prove. 15,000 LIRR commuters now have to make up and over and non-timed, non-guaranteed transfers at Jamaica for Brooklyn. Not a peep over that. They must think that is the Brooklyn in Oregon.