Both are based on Attermann's microReticulum library, but RTNode runs a vendored, customized version.
I've found the biggest practical difference between the two is that RTNode only runs on Heltec v4 and v3 ESP32 hardware, whereas microReticulum_Firmware runs on these two plus many other boards. Most significantly, it can run on the nRF52-based RAK4631 board which is much more power efficient. This makes it well-suited for smaller solar/battery-powered LoRa repeaters. Another useful feature it offers for remote repeaters is a nomadnet status page, and there is even early work on remote node admin over LoRa. It also has support for the RAK15001 flash module which makes the minimal nRF52 hardware more functional for storing RNS transport node routing tables on larger networks.
RTNodes are designed specifically to act a bridge between 1) LoRa mesh nodes, 2) local WiFi/TCP client nodes, and 3) remote internet/TCP backbone nodes (it also recently added Bluetooth bridging but I haven't tested this yet). Combined with battery-powered WiFi router/APs, this can create an access hub that allows anyone with a WiFi-capable device running a Reticulum app to communicate over a very resilient (and hopefully less likely to be bandwidth congested) hybrid of both LoRa and whatever TCP is still online/accessible. RTNodes can also still run on solar/battery, they just need to have a bigger power setup or they won't last as long in winter or otherwise less favourable conditions.
I will also highlight an important difference because it has caused problems for me during earlier rounds of testing: RTNode supports IFACs, but microReticulum_Firmware still does not! Therefore, for testing of LoRa repeater nodes, there can't be any LoRa interfaces with IFACs enabled if you're trying to use a microReticulum_Firmware node.