These ECUs are just very reliable, slow, expensive, specialized computers with input and output hanging off of them. I don't know what comp architecture they use, but at the end of the day, they are just readings bits from input and memory, doing some math, comparing some numbers, and pushing bits out to output and memory, the same as whatever you are typing these posts on.
Putting files on, pulling files off, and erasing files on the ECU is nearly as simple as copying files from your computer to a thumb drive. It takes a not-even-that-special cable that probably has a total BOM cost of 3 dollars.
The actual editing of the files is special. You could open the file in notepad, change some numbers, save it and push it to your ECU, but it wouldn't work right. You could spend hundreds or thousands of hours reverse engineering and designing a GUI that allows you to make changes to the underliying function of the ECU, or you can beg/borrow/steal the program and/or design software from Yamaha/Mitsubishi/whoever has it. I almost wonder if all of these low budget Mitsubishi ECUs are the same, and FTECU and Nate just leveraged past tools/efforts to change the tune. The Alba Nate thing is especially weird, considering his tune disables one of the fan outputs! It makes me wonder if it's because instead of FTECU he used some weird older software that only had one fan output and not two?
And, like all Software as a Service(SaaS), the 100 dollars per license FTECU charges is just revinue stream. There is nothing special about marrying an ECU, and was implemented to prevent you from sharing the $500 dollar $3 dollar cable freely with your friends(or shops from not paying licensing fees).