@Jessica Martin good question — and honestly the kind of thing that deserves a proper answer in the docs rather than making people dig for it.
The 2Mbps spec and the 50km figure aren't operating simultaneously — you're right to flag that tension. The 2Mbps is the data rate capability of the RF front-end at closer ranges, while the extreme range performance is achieved through the combination of external PA/LNA amplification and high receiver sensitivity, which is where the real engineering is. The modulation isn't something exotic or proprietary layered on top — it's working within the BLE stack — but the external amplifier chain is doing heavy lifting that no commodity BLE module has.
The honest answer on the LE Coded PHY question specifically is worth raising directly with Moamen in the SDK documentation thread, because the detailed PHY-layer configuration options are something he'd want to address precisely rather than me speculating on implementation specifics I don't have the full datasheet in front of me for. What I can say is that at 50km you're in the drone-to-drone scenario where both modules are airborne and ground reflections are eliminated — that's a very different link budget situation than ground-to-ground, and the range figures reflect that. The 5km ground-to-ground number is probably the more operationally relevant one for most builds.
If you're building something where throughput-vs-range tradeoff matters for your application, the AI Firmware Builder in the Dev Hub is actually a decent place to prototype that logic — you could describe your link scenario and it'll help you structure the PHY switching logic if the SDK exposes that control.