I have done merges for tens of thousands of people in the last several years and have never had a problem with designating whether to keep the old preferred as preferred, or to use the "new" merge data to replace the "old" preferred fact and make it an alternative one, or just add the current entry as an additional source for the preferred fact I already have. You might want to re-evaluate how you are merging - you have complete choice of what to make preferred in every instance I have found. If not, which database are you merging where you experience this?
I don't follow what you mean by fact "sort order"? All databases in ancestry are different and have different data to be merged. Census entries, for example, follow a natural order of Name, Sex, birth and residence. I don't see how making these facts merge in alpha order improves anything.