Update - I got a quote from a shop in northern-ish Virginia that does a lot of 4x4 builds, including a bunch of similar rust remediation work on Jeeps, Toyotas, etc. They are one of the shops listed on the STC site as an approved installer. So with all that and having visited the shop I feel pretty good that these guys run a decent operation. They advised putting the STC on both sides of the rear bumper area, including around the corners and into the sides of the frame. So 4 total STC pieces. There are also two smaller holes, including the one pictured above next to the cats and an even smaller one on the other side of the car, that they feel can be cut out and patched effectively. They'd then wire brush and POR-15 the entire frame (they'd do this for the new pieces regardless, having the whole thing done is an additional $650). They estimate 16 hours of labor, for a grand total of $3300.
Overall they felt like the rest of the frame was in pretty good shape - just surface rust and nothing at imminent risk of collapse or anything. So with the knowledge that I also need to do strut and possibly control arm replacements in the not-too-distant future, I'm probably looking at around $6k to have the non-driveline stuff in decent shape. Given that I believe the driveline is in a pretty good spot, I'm thinking it's probably worthwhile getting the work done. We almost certainly couldn't buy a better replacement for what we'd get for our 4runner as-is plus an additional $6k, and if we get another few years out of it before having to make another decision, I think we'd be happy with that.