The expensive portion of the mark and sweep for the object store is the mark phase, not the storage of what's been marked. 100s, 1000s, or even millions of live objects wouldn't hardly take any space to keep in a remembered set.
On the other hand, querying the S3 bucket to list those 1M objects would be expensive no matter how you store the results.
But this does tickle my brain. Perhaps something akin to the generational hypotheses can be applied? Maybe it's the case that very old, very young, or very untouched objects are more likely to be garbage than not. If there's some way to divide the objects up and only look at objects whose are in "probably need to be collected" regions, then you could do minor fast sweeps semi frequently and schedule more expensive "really delete untracked stuff" infrequently.