combine 3 phase 125 amp dock power into one 250 amp shore cord?

In theory, yes.
In practicality, NO.
Safe, Absolutely not.

Either split the ships loads on two (seperate) 125A leads or install a power controller like a big Atlas.
Either way will still require 2 x 125A leads.

A “big boat” with 250 Amp shore power must have some type of shore power system to allow various configuration, doesn’t it ?

The smart Y works for smaller loads because it’s only handling single phase output using opposing phases to balance the increased load. This setup won’t work if phases are inline, and Hubbell rejects the B outlet and won’t stack the amps. I don’t see where that technology can work in a Y setup. Seem logical that it can only be managed by an on-board power system navigating two cords. If you think about it, you’re pulling 125 amps from an outlet wired for 125 amps and no extra leg to share the extra 125. If a Y could do that you’d be pulling 250 through wires intended for 125. That wouldn’t last long……

reverse Ys have circuitry to allow pulling from two receptacles and combining the output. Works pretty well when connecting a single phase 100 amp inlet to two 50 amps outlets. The circuit will only allow the connection if both legs are connected to compatible outlets.

Yes, I have Hubbell's smart Y for the 100 to two fifties. Ive never seen a unit for two 125's. Ive only witnessed vessels using two 3 phase cords and managing loads aboard.

FWIW, Hubbell's smart Y allows for in phase outlets to serve you with 50 amps alone, whereas Marinco won't function if the outlets are in the same phase.