Reporting on more Paragon usage 'n all that: was playing through chapter ten CQ, and Selena and Beruka spawned in without any stat changes (Except weapon ranks for some odd reason). I did some perusing to troubleshoot, and I figured out that they were spawned in the chapter data under the name PID_B_(name). Additionally, the UI element that paragon shows when referencing a character didn't show up. I changed that to PID_(name) which is the standard template; the UI element showed up and they still spawn in the chapter normally but with all the changes applied!
In CQ route, only Selena, Beruka, Kaze, and Shura spawn with the PID_B_ prefix. Unsure of why or any ramifications of changing it, but it seems to mess with Paragon's interactions.
Anyway, will update if anything goes awry!