Mud,
I see that your 4350 has the Fwd-Rev Synchroshuttle/full Synchromesh transmission. Do you have to step on the clutch to change from forward to reverse? That transmission is a little more technically advanced

than the transmissions in our 3525's... I'm betting that if you don't have to clutch to change direction there's a big clutch pack in there for the forward/reverse shuttle, if not, a big heavy duty synchronizer, and then synchronizers for each gear as well. During break-in I'd bet that there's a lot of stuff that comes out of that clutch pack as it wears in and gets comfortable with life. They probably want you to change the transmission oil at 50 hrs to get that contamination out of the transmission so that it doesn't affect the synchronizers and the clutch pack itself long term.
I doubt that being 4wd has much to do with it, as that's only just another gear or 2 spinning around in there.
On our 3525's, there's nothing technological in our transmissions at all... no synchro's, no clutch packs, nothing but big ol' gears and bearings. About as basic as you can get. So I guess they figure that not much is going to change in the first 1000 hours of it's life, so no need to change that oil right away.
Enjoy your 4350, that ought to be a great little loader tractor!!