First, the FTM Fact Namesake is meant to be the name of the person for whom this person was named. For example, Winston Smith born in WWII might have been named Winston after Winston Churchill. The entry in that fact description would be: Winston Churchill. Note that the namesake field does not bifurcate prefixes and suffixes like the Name Fact does.
Secondly, as for Jr and Sr. Following is "My Practice" A different practice may work for you.
I rarely use either as the PRIMARY name used in my database. When I do, it is usually 20th century folks with rather unique names. Of course, I will enter the name as it is recorded in documents as an Alternative Name, when found. (That name will show up in some on-line indexes of your gedcom file - for example WorldConnect includes alternative names in their names index, but FTM doesn't.)
I have found that in my surname study I have enough of a problem with finding who I am looking for among the 75 fellows named James Taylor, James A. Taylor, James Brainerd Taylor, to middle initials beginning with Z, then the 10 fellows named James Tailer, and on and on. I have to look in each "grouping" to find a guy I might be looking for. Adding a suffix to the mix just creates more groups.
How do I tell the 25 James Taylors apart? First by their birthdate and then by spouse, birth or death place.
Besides, some fellows might be without a suffix until married, then a SR after a JR is born, but in current day nomenclature is not actually SR because it is not on the father's birth certificate; which has no relevancy to father's born before 1900 since the concept of birth certificates is mostly a 20th century innovation.