Update: the bags made the 11:30am nonstop CLT-PWM and were promptly scanned in as stored in the baggage office in PWM, beating rerouted wife+kid by 7 hours and beating me by 9 hours.

Takeaways:
-SJU is no different from other domestics in the lack of passenger-bag matching
-Unless you really need the bags (or don't want to risk someone yoinking them when they're circulating on the belt forever), it's fine to just let them fly the original routing and meet you later
-Wife+kid are much happier than they would have been if they had to get the bags at CLT at 1:30am, shuttle to a hotel, shuttle back at 4:30am to check them, etc. They actually enjoyed the Spirit experience (everyone was apparently super friendly, both FAs and fellow pax, and they were able to carry diaper bag, stroller, purse, etc., with no fees, so SJU-TPA last-minute was only $130 including a seat-choice fee). And the TPA Marriott graciously extended my ambassador perks to them (F&B credit, lounge access, suite, and late checkout) even though they didn't have to, since I wasn't staying.

She will needle AA on AA.com about the (still relative) PITA and will likely get some miles thrown her way to offset the 25k miles I spent on her first class TPA-DCA-PWM award getting back this afternoon. All in all, not terrible.