Soothing Familiar prerequisites broken

One isn't allowed to take [Soothing Familiar] from class features when one has acquired the origin feat [Familiar Friend (Charisma)] from the Human [Versatile] ability. 

I assume most of the feats that require [Familiar Friend] like [Warlike Familiar] are similarly broken. 
I just checked, and [Warlike Familiar] works as intended.

You're correct that the feats are broken.

* If you pick Familiar Friend, only Soothing and Otherworldly are available..

* If you pick Familiar Friend (Wisdom, Intelligence, Charisma), then the matching Elemental (Wis, Int, Cha), Warlike (Wis, Int, Cha) are available.

I can also theorize as to what happened here from traditional Beyond limitations.

The background uses the attribute-less version and lets you pick an attribute from the drop down. The "pick it up later" has three versions - and then they've got that chained through to the three stat versions of Warlike, etc.  The workaround is to add the correct attribute feat as well as the generic one to the sheet. I haven't tried the other way, but would theorize it probably works.

So the issue is they need three copies of the background keyed off the attribute versions but opted not to do that. Since the stat choice doesn't have any impact on the familiar's stat in the extras tab, the workaround is just to add the specific attributed feat as well to get the tree working as intended.