Not sure really. Do you know for a fact that it does not already have the correct setting?
Doing a step back, the reason why you had to load "cape-universaln" is because it was require by your python script. However, you do not actually need that overlay and it seems that it is causing troubles elsewhere. You could try to edit the script so that it is happy with the
BB-PWM1 overlay, then load that and your eqep overlays by hand.
The edit should look be just a new line like:
|| device_tree_loaded("BB-PWM1"))) // ""
Incidentally, I have no idea why that python script used to work in the old image, maybe it was a different version of the script? Or there must be something that I overlooked while going through the script, because among the overlays loaded on the 0.1 or 0.2 image there is no
4: ff:P-O-L Bone-LT-eMMC-2G,00A0,Texas Instrument,BB-BONE-EMMC-2G
5: ff:P-O-- Bone-Black-HDMI,00A0,Texas Instrument,BB-BONELT-HDMI
7: ff:P-O-L Override Board Name,00A0,Override Manuf,BB-SPIDEV0
8: ff:P-O-L Override Board Name,00A0,Override Manuf,BB-BONE-PRU-BELA
9: ff:P-O-L Override Board Name,00A0,Override Manuf,BB-BONE-BAREAUDI
Note that I am not suggesting that you load these, I don't even know if they are still available on the newer image (surely the BELA one is not).