You might want to PM Sir Sam as he has been all the way into the water pump and I have not.
That said the 2 cam pins and the flywheel pin are used to make sure the cams and the flywheel/crank are timed together which makes the engine run properly and, most importantly, keeps the valves and pistons from occupying the same space. If you are just doing the timing belt (not including the water pump) you don't really need the big shiny aluminum cam sprocket holding tool although IMHO if you have one, I do in my full Miller kit, you might was well us it. I don't recall if the top edges of that tool engage upper cam teeth (I think they do but just am not sure) but I do know that the bottom knobs are used to engage lower cam teeth (i.e. lock not adjust). As I understand it the main purpose of the tool is to hold the cam gears and cam shafts stationary relative to each other while the cam nuts are being removed and reinstalled. The 3 pins are simply not up to the job of doing so. The cam gears are not "keyed" to the cams so the cam gears can bolt back on most any way, the same position the came off is IMHO still best, but it's critical that the cams and flywheel remain in the same relative postions.
That said
http://www.beesvillebeefarm.com/jeep.html used a VW cam holding tool and I recall a forum post, don't have the link, where someone used some combination of welded angle iron to lock the 2 cams together during removal.
Sir Sam and others would likely know better than I but I suspect locking the 2 cams together during removal is not critical, rather it's convenient. Seems to me, pending ratification, that each cam could independently be held stationary and removed/reinstalled so long as when done the witness marks and 3 pins all lined up properly. NOTE this opinion is just that until ratified so don't depend on it.