Preferable for the customer, sometimes. But not always, and not for the manufacturer.
125A breakers are not as readily available as 40A breakers for some panels. Even when they are, they often cost a lot more. 15, 20, 30, 40 and 50 amp breakers are all typically around the same price. Going for 3x40 works on almost all panels. Unless you're totally full, in which case you likely can't spare 120A of current anyway.
In addition, the design may be easier to use 3 heating elements instead of 1 large heating element. Allows for partial heating, smaller controls, etc. Once you do that, splitting the supply makes sense.
Finally, wrestling 125A capable cable around in a basement is a LOT harder than 40A cable. Doesn't matter in a new house but often goes in a retrofit.
To answer the unasked question: Do I have enough capacity in my panel?
Having enough spaces - whether for 3 x 40A or 1 x 125A - is only one of the parts of the answer. You also need to have large enough electrical service to support 125A of water heating. You may have 200A service but already be using on the order of 150A, in which case a net gain of (optimistically) 80A (i.e., adding 120A but subtracting an existing 40A from the tank heater that is being replaced with tankless) just won't work. You'll trip your main breaker occasionally and your utility will complain too. Or you may have 200A service but actually only use 80A because it is a small house with some gas appliances and no bitcoin mining or grow lights, in which case a net gain of 80A to a total of 160A will, just barely, work. This is a truly major change in your electricity usage and, unlike the other common change, electric vehicle charging, harder to manage. Hmmm, I'll charge the EV at night only (easy) and use the hot water during the day. Then someone gets stuck in traffic for hours (happened to quite a few people in Virginia recently) and come home in the middle of the night and take a nice hot 120A shower...and suddenly everyone is in the dark. Load calculation, possibly followed by an increase in your electric service, is necessary. And hope you never get peak demand charges.