I dont use the EBB boards, but I have used the Mellow 3D equivilant, and have settled on the MKS ones (RP2040 Based) mainly as I get these very cheap and I prefer the larger JST connectors, I have used both CAN and USB with them, both work fine, the fuss with the cabling for such a short run is not really required, I tested several self made cables, twisted, not twisted, outside the printer, umbilical and through drag chain, there wasn’t any major issues I came across, with both CAN and USB.
I also seen no point in CAN over USB, not for what most of us do with our machines, so the added complexity and additional hardware, I find CAN pretty pointless, one of my machines runs 2 x control boards, 1 x tool board, 2 x cameras, 1 x Wifi all from a USB hub connected to a single USB port on the host and there is no issues, I do have to increase the TRSYNC, but that issue is also there with CAN and is not actually releated to data coms corruption.
I also have no issues with restarts, reboots, cold or hot, with the exception of 1 machine that uses a x86 USFF Dell PC, that requires USB power to be cycled after it has booted, and I use a USB relay and a script for that.
Not sure if the EBB is the same, but if you have issues with the tool board starting after a firmware restart, try cyclng the toolboards power, instead of a full reboot, either connect a manual switch to the 24v feed or use a USB relay to toggle its power, alternativly hitting the reset button on the toolboard will also make it recover.
The little Voron Im currently working on also has a MKS-PI Host controlling 2 x Printer boards and 1 x Toolboard for a multimaterial setup, all over USB, the external MM unit has BTT E3 RRF in it, and I do the same as my tool boards, I just mount a USB 2.0 socket in that and break out the data wires and power seperate, so all I need is is a USB-A to USB-C 2.0 cable to run and to power it, and that MM box has 4 extruders on it, USB is very reliable, and we have been using it with Klipper for many years.
Im still not seeing any reason to use CAN instead of USB so far.
On a side note, I would love to see a toolboard that just has 4 x mini screw terminals instead of a USB port and that silly Micro fit connector, you can just have 24v/GND/D+/D- and your done, they could also incorperate a USB 2.0 hub so you could potentially run a USB camera on the tool head, you wont be doing that with CAN.