The price difference would be peculiar if you were comparing oranges with oranges, but you're not. One service centre is recommending replacement of all fluids; the other isn't.
That isn't all that surprising for any car. Some service centres for a given make may recommend, say, a fuel system flush with each service, while others say it's okay every second or third service. Some will insist on wiper changes on each service; others only "as required".
I guess the real question to forum members is, if your IS 250 hasn't been serviced for three years, but has only been driven 7,000 km (and somewhere between 7,000 and 12,000 km since a major service), is it really necessary to replace more fluids than just the oil? (Sure, there are good reasons for changing oil at least yearly, but that isn't a factor here, as it's going to be replaced even in the most basic of services. What about coolant, brake fluid, ...?)