Boeing didn't agree (or not) to anything. The aircraft is certified for a maximum number of seats and the operators are free to use any configuration they wish, provided they don't exceed the maximum (and meet other regulations)
Your issue is with the airline, not Boeing.
Not all B787 operators configure their aircraft the same as the one you were on. Use Seatguru or similar web-sites to check before you pay.
Oh, and you could pony up and sit in Business or First class if you really want a comfortable flight.