Hello D.D. and thank you for your detailed answer.
First things first: I am building - well, have actually completed the built - of the aluminium version. And had in mind since the begining that I would then try the full 3D printed version, less stiff but probably much lighter, in a second step if I feel confortable with V.1 (our project is to mount a robotic arm on a wheelchair, so there will be quite some hacking on the AR3 current 3-tier architecture (arm / enclosure box / control "big" box).
As for my wiring problems, they originated from the fact I was following the instructions of an obsolete version of the manual (I downloaded it in jan 2020 and a revised version had been publised since).
Chris Annin is kindly helping me on that matter.
So, if I'm not mistaken, the GX16-2 should be connected directly AND only to the Vin and GND upper ports of the Teensy, and the Teensy should be powered only via the USB connection to your PC. In other words, the encoders and limit-switches are powered via the Teensy and share the same ground with the said Teensy.
The 5vdc power supply is only needed - I guess - for the Mega, and in my case, I will have a limited use of the Mega and probably none of the 8x Relay board, since I plan to use an electric gripper.
I still have a couple of tests to perform today, guided by Chris's instructions, and I'll keep you posted.
Kind regards,
Pierre