This weekend I did the 50 hour service on my Kubota M8540HD. It is a Hydraulic Shuttle transmission.
My book called for the hydraulic fluid to be completely drained (along with filters and engine oil of course). My dealer said I could probably get away with just filters, however I wanted to do it "by the book" per se.
When I pulled my filters off, the magnetic rings had quit a bit of metal shavings on them. Not enough to cause me any concern, however it was enough to make me happy I was swapping the fluid. When I was transferring the drained fluid back into the empty containers, I noticed a lot of tiny metal bits in the bottom of the drain container. Again, no conern but am glad I changed the fluid.
I don't think anyone disputes the fluid itself still has life in it. The main reason to drain the fluid at 50 hours is to get out the bits of metal floating around in there. There are a lot of parts breaking in and seating to each other: gears, clutch packs, main brakes, pto brake, pumps, etc. The filters cannot get everything.
I think it is critical to go by your manual. Not all tractors are created equal. Not all "same brand" "same size" tractors are created equal either. Transmission types probably have some factor in the manufacturer deciding what needs to be changed at the 50 hour mark. I would guess hydraulic-type trannys (hydraulic shuttle, HST, etc.) probably require a full drain more so than a straight gear with standard clutch type tranny.