Prior to v3, these were independent from each other. Now, they seem to be dependant; what has changed?
do you mean the opposite? before by default they were linked. now they are independent by default. AFAIK the latest thinking goes that you should leave the noise threshold at 0.005 and just tweak the colour threshold and MSR (or the noise threshold limit and MSR in progressive)
That’s correct the Use DMC Sampler Threshold has been removed in the latest service pack, the idea is use Color Threshold value in order to set up Image Sampler instead changing the default DMC Settings.