Assembly features are quite useful however there are potential drawbacks. Adding assembly features can dramatically reduce assembly performance. Every time there is a change in the assembly the Assy-features will update. Depending on the number of features this update can takes several (read 4-5 in my case) minutes to update. That means: add a single contraint - update, move a part - update, unsurpress a component - update....you get the idea.
Using the EOP roll back is helpful but not a full solution. That's because the EOP roll-back effectively supresses the assy-features which causes and constraints made applied to those features to fail. Dismissing constraint failure dialog boxes gets pretty old rather fast.
I would suggest to ADSK to add a new option to assy-features that allows updates to be suppressed but the feature to stay active. Perhaps you could point to the assy-feature>RMC>properies and chooses "suppress-updates" and then see a lightning bolt or something. That would be similar to suppressing updatr in wire harnesses which works rather well.