Some options. There may be more
1) Continue to let FTM databases post name variations to the name fact, but mark them private after merging. (Select the name fact, right-click, private).
2) You can always make a name disappear in a merge (by using the discard option), but if you do that, you would normally also uncheck "Post the source anyway" box if the name doesn't agree with your primary.
3) You can keep the source for the name variation and put the spelling variation in the source citation - text box.
4) Keep running track of names and spellings used over a lifetime in notes under heading "NAME", then list birth name, first census name, 2nd census name, etc.
Over the years, I have used variations of all of the above, but have finally ended up just letting the name and all variations flow though merges from ancestry databases. I now have a complete running history of all names used by a person in a lifetime that way. I have found that comprehensive list is the best way to evaluate what name to use as preferred after you have found most records. You can right click - Merge facts to merge identical names. This is particularly handy for merging exact duplicates of married names of women.