Using the "Also Known As" fact has effects in FTM in two places: 1) the index and 2) reports.
1) The index -
a) the PREFERRED aka can be included in quotes between the first and middle name of a person.
b) the PREFERRED aka can be included in the index as a separate entry (this will probably slow your program operation down.)
Other AKA facts that NOT preferred facts will have no impact on the index, whether in quotes or as a separate entry.
Using the Genealogy (register) Report, a name can have the PREFERRED aka in quotes in between the first and middle names in the opening paragraph of that person's "sketch".
NON-PREFERRED AKA's are presented in the "other facts" section (which can be a list or a paragraph) in a sentence as: WAS ALSO KNOWN AS
NON-PREFERRED NAMES are presented in the "other facts" section (which can be a list or a paragraph) in a sentence as: HE/SHE ALSO WENT BY THE NAME OF.."
Effect on WorldConnect presentations.
Worldconnect will read gedcoms and present an index of all names, both preferred and not preferred, but no "also known as" names.
As for myself, I gave up on FTM's complete compatibility to gedcom years ago. As Bruce Willis said at the end of his sketch in Pulp Fiction: "Zeb is dead, baby, Zeb is dead". That kind of sums up my feelings about gedcom.
So, I enter data with the primary priority of how that information will appear in FTM reports, not be compatible with gedcom.
I record nicknames and variations of a first name as aka. I rarely will put a surname as also known as. I record EVERY instance of a name that a person uses in their life, no matter how it is spelled - as a separate Name fact.
That's not to say my practice is right or wrong - I'm just throwing my practice out there.