Yes, the TTTE phase will pass. You might refer to DS2 as Baby Tommy or something anyway for the first year, so DS1 won't connect it, and then by the time, you're calling DS2 Thomas, DS1 will be on to Spiderman or something.
Clear consensus then - now I just need to convince DH on the name!
I can't overemphasis the level of obsession with the tank engine - it's practically all he talks about - but yes it does seem absurd to dismiss a name that will last a lifetime over a toddler phase. Calling the baby Tommy at first is a good idea though.
My boy loved Thomas too. If I'd asked him what to call a new baby he'd have probably said Thomas, or Percy, or possibly Diesel 10. He's 10 now and well out of the other side. I think your DS will love it if you call your new baby Thomas.