Connecting Lora and FSK clients to a single server
The SX1278, as the first page of the datasheet tells us, is an SPI device.

The Pi has GPIO pins that can be configured to be SPI pins. Based on the SPI interface the Linux kernel then offers to userland programs, you can write your own software that talks to the SX1278. That'll require a bit of understanding of how SPI works, reading the datasheet and basic programming knowledge.

If you're more for actually integrating that module in the Linux 802.15.4 infrastructure, https://github.com/starnight/LoRa might be an interesting project. This goes more in the direction of LoRaWAN; I personally think that you've got similar problems to what LoRaWAN solves, so your easiest course of action might actually be using that for your LoRa devices.

AES encryption on a Arduino is very likely not happening - "arduino" is but a family of devices running a family of firmwares, based on very different microcontrollers, but even the most capable ones among these microcontrollers are very limited in RAM: If you find an AES library running on the microcontrollers, it's very likely you'd want to abandon the Arduino layer and just directly work with that, as you'll have to deal very efficiently with the limited resources you have. Arduino's sketches and libraries are certainly not the way to go there.

Overall, you don't seem to have a very firm grasp on what the capabilities of the devices you're considering are; for example, the NRF24L01 is a deprecated device, but there are plenty of similar controllers that both integrated the modem as well as a microcontroller. Maybe that solves your issues with lower component count.