ButFli - it's not just for the backtracking 04/22 scenario; that was an example. It's a general-purpose "skydiving takes priority" thing, to essentially keep 04/22 clear of very slow traffic. If the skydiving planes have priority access to 04/22 and the adjacent run-up bay (which is also where they pick up skydivers) then that's obviously good for the skydiving operation.
As for why it doesn't apply to aircraft less than a certain weight - not sure. The possible reasons I can see are (a) bigger planes tend to be faster (getting stuck behind a C172 isn't quite as bad as getting stuck behind a Gazelle), and (b) bigger planes may not be able to use the grass strip, while I suspect that anything under 650kg can.
Ultralights - presumably they've had problems fitting in with other traffic, if they went to the trouble of setting up the NOTAM. Obviously it's always possible to fit in with other traffic, but it may not be cheap or easy - especially when the speed difference is as big as it is at Goulburn (between the Bandeirante and the Gazelles).
Regarding the right to land before anyone else - I agree. It's not a right that bigger planes and/or commercial flights get to land first. However, from what I've seen (around Goulburn, Moruya, and Wollongong) it is a reasonably common courtesy.
Commercial reasons justifying a NOTAM - I would think that the owner of the airport can do more or less whatever he wants here. Closing the whole airport, requiring prior permission for any airport operations, restricting use of one runway, etc. Other airports (eg. Mittagong) require prior permission; what's been done at Goulburn seems like a less severe restriction than that.
Hempy - the run-up bay doubles as the skydive loading area. It's not great, but it's probably the only spot that avoids having skydivers wandering around on the taxiways. The obvious consequence is that there always needs to be space in the run-up bay for the skydiving planes to get in, and if someone parks right in the middle then there won't be.
Realistically, they should probably just rename that to the "skydiver loading area" and stop calling it the run-up bay.