The reason is absolutely that Yamaha does not want to go the cost of making a bone saddle.
I recently replaced the saddle on my Yamaha guitar. The factory saddle is a plastic casting that takes zero hours of labour to make. I doubt they do anything to the saddle after injection molding it. Maybe they sand the bottom to adjust the action. It fit very loosely into the bridge slot - so loose that it was tilted within the slot. No doubt the injection mold is planned undersize so that they don't have to adjust any of the saddles to fit into the slots.
A bone saddle requires that 1) the bone be prepared and cut oversize, 2) the bone be adjusted until it is reasonably straight (many I've bought are not straight), 3) the bone must be thicknessed to fit neatly into the bridge slot, 4) the upper surface must be profiled to get the desired string heights at the 6th and 1st strings, 5) the profile must be filed for intonation correction, 6) the bottom of the saddle needs to be filed to set the string action, and 7) the saddle must be polished.
Even an expert worker will require time to do all of this. Much cheaper to just thrown a cheap plastic piece in there and call it done.
As for my guitar....I adjusted my bone saddle and improved the action and playability....but it didn't sound any better than the plastic saddle supplied by Yamaha.