Unfortunately, this is a problem that isn't going to be fixed (at least not in the near term) by the new searching arrangement for variant surnames. I submitted freke and ffreke as a matching pair at http://www.werelate.org/wiki/Special:Names and got the message "The following rare names have the same soundex code, so they will be matched automatically: ffreke." That means they won't be added to the werelate database that's used here.
But if you add the alternative spellings to individual profiles as "Other Last Names," the WikiTree search should find them and prevent some duplicates from being created.
To ensure that Freke (or Foote) is the merge destination, I suggest that you request temporary project protection for the individual profiles that you want to merge to.