Unable to interface BeagleBone Green with MCP3008 ADC using SPI
I don't believe the beaglebone green is 5V tolerant, thus the 4.1V output signal of the ADC might be harming the device.

It would take some real time to see if this is correct, but I suspect it is.  The Beaglebone Green is based on the ARM Cortex A8, specifically THIS FAMILY.  Absolute maximum ratings on page 79 show that the max voltage at I/O pins is supply +0.3V.

That's the easy part.  Now, what is the supply voltage.  Unfortunately, this doesn't mean the voltage you supply to the board.  It means the supply voltage sent to the microcontroller.  The board uses regulators to drop down the supply you give it.   We could go through the Beagleboard Green Schematic and really try to pin this down, but the A8 is fairly complex and has MANY different power supplies for many different things, as you can see by all the VDDS listings in the absolute maximum table (from the datasheet link above).



Without trying to trace the schematic, or actually reading the data sheet to find out why there are so many different absolute maximums for the "supply voltage for the dual-voltage I/O domain", you'll see that the highest number in that class is 3.8V, which suggests that your input high cannot exceed 4.1V, assuming that the Beaglebone Green provides the highest supply voltage allowable (which it may well not!).  In fact, first glance at the schematic suggests that some of the VDDSXXXXX lines get 3.3V, and others get a voltage that comes out of a TPS65217C Power management chip (though that latter might be an input to that chip -- I can't chase this down through all the datasheets, as it would take too long).

It looks like you went outside the allowable limits for the pins.  This doesn't necessarily mean that you broke those pins, or that the whole system is kaput.  If it were me, and I had only this board available, I would try using a different port with some interface circuitry to step your inputs down.  That said, starting with a fresh board is a better guarantee that things are good.  It can get very frustrating debugging stuff like this when you don't know for sure that your hardware is good.

So, this was somewhat difficult to run down.  Beaglebone is a great board with nice features, but the user base is much smaller than that of the Pi's, so this info wasn't readily available by searching for it.