Several years back NYS adopted the FMCSA rules in their entirety. The Legislature had no clue what they were doing, but there you have it. So, now all commercial vehicles in NY need to comply with FMCSA rules that apply to them. The DOT # is issued and ID's that vehicle as a intrastate unit. As far as I know, there is no cost for getting the number. I'm not aware of any costs that would be any lower since the same equipment and everything else is the same as for an interstate vehicle, except for IFTA and similar taxes.
I was a NYSP DOT Inspector for the last 6 years of my career. You aren't the first guy to wonder about this.