I've changed the sleep/delay code on jdolecek-ncq branch so that the sleep is always at least 1 tick. You might give it a try - if that is really the only issue, this might help. Increasing the timeouts however did not fix the issue for me on 60xx, at least not with the brief testing I did so far.
I've experienced the EDMA timeout on 6048 just while booting or some light use, while it almost never happened on 70xxx. It usually happened when the chip was wedged for other reasons, like unrecovered NCQ error or some such. So I think that there might be something else we do wrong for 60xx, and the EDMA disable problem is just consequence.
60xx was however not really focus of the NCQ branch, and I won't do anything further for it on the branch. My focus is now on completing my branch and merge, and some RL stuff. Then I may start looking on the 60xx issue, but that won't be before late September.