Real Prime Battery Capacities

That's exactly what I saw in the app for my 2021 Prius Prime Limited, with 6.3 kWh being the assumed 100%-SOC energy at the 240-V plug. Just like you said, the SOC values used in the charging kWh estimates were identical to those shown on the MID—therefore, correct—but the instantaneous SOC values shown in the app were all over the place and made no sense whatsoever. Therefore, there is a bug regarding the instantaneous SOC values shown in the app.