I suppose the problem is exacerbated by the fact she's not peak level normalise which, as mojave pointed out in another thread, adjusts the level for intersample peaks.
I agree; volume leveling also solves a lot of these problems.
Ultimately I think this is one of those things where jriver lets the user shoot themselves in the foot. A nice, if somewhat niche, enhancement might be if audio analysis were DSP aware, i.e. you could assign a DSP profile to a track (or inherit it from a zone) and then audio analysis runs with that DSP applied and then can adjust levels automatically to keep the signal clean.
You're right that you'd basically need to reanalyze all of your content to make that possible (It's hard to predict if a given combination of DSP would cause a track to clip in advance without doing analysis).
Honestly, I'm not sure a more sophisticated solution is really necessary as all any such solution would do is just turn down the volume a bit, which:
a) a user could easily do themselves on demand in a way that addresses their situation (either permanently in the DSP chain or on demand using the actual volume control).
b) If you enable volume leveling or adaptive volume with peak level normalize, you get a 90% solution as they both attenuate tracks a minimum of the amount of 1dB + whatever is needed to avoid intersample peaks, and volume leveling will often provide even more headroom.
c) And if things get out of hand clip protection will catch any oops's, by turning down the volume on demand.
Basically, it all comes down to turning down the volume some when using DSP. If I were facing this problem, I'd probably rather just dial in a permanent -2dB for all channels in PEQ rather than reanalyze 80,000 files