At first glance, it looks like they want that merc affiliation to only apply to character born into the life, and that for a character that becomes a merc later, you'd stay with your original affiliation.
On the other hand, the second read suggests the opposite.
That little note at the bottom of the chart on page 63 could really use some clarification.
"Characters that are not born to the mercenary life but turn mercenary later must choose another affiliation as well."
"Characters that are not born to the mercenary life but turn mercenary later must choose another affiliation instead."
Both acceptable, both meaning the complete opposite.