I've tried a few different flavors of linux on my laptop and all can pair and connect and run Ekos/Kstars with very little trouble. Mint, Ubuntu Mate, Lubuntu and even Peppermint all do just fine, just like my windows machine. At least I have that going for me, I can always leave that laptop outside and VNC into it with my windows machine.
Raspberry Pi is a whole different story. I've tried Ubuntu Mate and Lubuntu on 2 different Raspberry Pi 3's, and nothing will allow me to connect. Bluetooth pairing works, binding rfcomm works via command line, and /etc/rc.local, but I get the same error I've documented previously in this thread. Every single time, no matter what steps I take to detect, pair and assign a serial port, all goes well up to the actual point where Indi tries to connect to the Shoestring dongle.
I'm going to try and find another RPI OS that may work, and in the meantime I'm just going to take my linux laptop back to Mint, it was my favorite flavor and I ran it for years. As for the raspberry pi 3 issues, it's beyond me. Doesn't make a lick of sense, and the same issue cropping up on 2 different machines and 2 different operating systems is mind boggling, especially with people claiming they get the exact same hardware to work on their machines.