Sorry, can’t help you there! This course, as any other guitar oriented one out there, is based on centuries of the technique that has evolved around the harmonic possibilities of the guitar’s conventional tuning. From the moment you change that tuning you are going to find yourself reinventing the wheel and redefining the instrument. Yes, you will find some new possibilities but then again you will find that many interval combinations are then not possible, especially in in the context of chord voicings.
You mention the complications of C-A-G-E-D and 3 Notes per String, but if you want my honest opinion, you’re faced with a whole new set of complications when changing the tuning. Trust me, if it was easier, we would all be doing it!