Side note, it appears Thalaviar made mention of his way to correct the 
4.14-ti kernel issues. his method was to :

git clone https://github.com/RobertCNelson/dtb-rebuilder.git
git checkout 4.14-ti
git checkout origin/4.9-ti -- src/arm/am335x-boneblue.dts
git checkout origin/4.9-ti -- src/arm/am335x-bone-common-universal-pins.dtsi
make src/arm/am335x-boneblue.dtb

This corrected the pruout/pruin pins that were set as GPIOs. one of the 
files was missing to rebuild it straight(if memory serves me, it was 
am335x-boneblue.dts). Not sure if this helps.

The adafruit bbio library allows access to any of the pins, but does it 
with the defacto config-pin in jessie and stretch. meaning :

https://github.com/beagleboard/beaglebone-blue/blob/master/BeagleBone_Blue_Pin_Table.csv

any of them COULD be accessed by knowing the header/pin number. In an ideal 
world, that'd be the pin list, with the references to the BB, BBBL "pin" 
and the actual ball on the SOC. for instance, as it stands right now, any 
of the Analog Ins, isn't accessable at all. Being limited to check AIN5 and 
AIN6 only via a C program is a pain. RCPY doesn't bring out the AINs at 
all. Show-pins shows nothing for them. they just don't exist. It can only 
be done in C, and with Libroboticscape. The rest of the pins on that list 
that are tied to a function in libroboticscape show up in showpins with a 
few bizare caveats(like motor 2 direction pin B), but have no way of 
accessing them because they aren't in any of the overlays. Libroboticsape 
does everything with them, setting them, and using them in low level 
programming. In a perfect world, the overlay would allow them to be brought 
out so we could use them with things other than LibRoboticsCape.

The caveat to this is your prior fears would be well founded though if a 
universal fix for them would break the use of libroboticscape(and the 
battery monitor that relies on it and it's analog pin mmap-ing).

While we can't expect you to test everything, I can give you a few very 
specific examples where it completely breaks down using adafruit's BBIO 
library in either tyhe 4.14 or 4.4 kernels. Give the ADC or PWM sample code 
in the read me a try.

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