the pilot bushing keeps the trans input shaft properly lined up, otherwise it'd be flopping around, and it provides a "wear surface" that acts like a bearing, they can wear out and get loose - the primary reason to replace the 2 [and the clutch pak as well] is so you don't have to pull the trans again when any of them cause problems a short while down the line ... and throw out bearings can have a shorter life than the clutch disk depending on how the operator treats it ... if all have been recently renewed, then switching transmissions doesn't necessarily require the rest, although it's prudent
Bill