@William Johnson good question, and you're thinking about this the right way.
The 50km figure is drone-to-drone with ground reflections eliminated, and yes, that's going to be on Coded PHY with the external amplifiers doing their thing — you're not going to hit that on 2Mbps PHY, that's just physics. The spreading gain from Coded PHY (125kbps S=8 coding) is what makes the link budget work at those distances.
That said, the RF front-end and the PA aren't locked to Coded PHY. The amplifier circuitry operates at the hardware level — you can run elevated TX power on 2Mbps PHY, you just won't get the same range because you've given up the coding gain. What you'll get is noticeably better 2Mbps performance compared to a commodity BLE module at default power, which typically maxes out around +8dBm and has no external LNA on the RX side. The MultiNav Pro+ has the external amp stack on both TX and RX, so your 2Mbps link will outperform a bare Nordic or Silicon Labs module at comparable power settings.
Honestly the best path for your use case sounds like PHY switching based on operating mode — high throughput when you're close and need the data rate, drop to Coded PHY when you're pushing range. The STM32WB07 at the core supports PHY update procedures mid-connection, so that's workable in firmware. If you want to dig into how to implement that, the Dev Hub AI firmware builder is actually pretty solid for generating the connection parameter update logic.