Having seen The 12 Monkeys, I can say that PIC Season 2 is very much a Terry Matalas show. I've also re-watched the two seasons back-to-to-back. I'm taking a brief pause from a Season 3 binge and I'll say there's nothing Terry ignored from Season 2.
The Jurati Borg are a different faction of the Borg than whatever's left after Janeway defeated the Borg Queen in VOY. And now that the Evil Borg, or the "the real Borg" as Shaw called them, are out of the picture, the Jurati-Borg are the ones still standing.
And Shaw, by the way, is an asshole who craps on everything 99% of the time. So I wouldn't read Shaw taking pot shots at the Jurati-Borg as anything more than what it is: Shaw's an asshole. He takes pot-shots at everything! Once again, in Shaw's first scene in PIC S3, I wanted to punch him in the face again. Then I reminded myself, "No, no, no, Picard and Riker are stringing him along."
Terry Matalas is a fan of the TOS Movies. And do you know what the TOS Movies did? Something different every film. Not because "the last one sucked!" but because "we want to do something different this time!" The only two exceptions to this were TWOK where they thought TMP was boring, and TUC where they quietly ignored TFF and focused on a story that served as an epilogue to II-IV.