Are you trying to build a hosted flavor of AROS on one of native targets, like RaspbeerryPi?
Here is the configure line I used in the past. Notice that I'm building outside of source tree, while you are trying to build in the source tree. In general this should not matter, but you never know if there is no regression. Also I used this line from x86_64 linux for cross compililation, while you are building native so some paths have to change I guess.
../AROS/configure --target=linux-armhf --enable-includes=/usr/arm-linux-gnueabihf/include --x-includes=/usr/arm-linux-gnueabihf/include --x-libraries=/usr/arm-linux-gnueabihf/lib