At first, this looks similar to issues we’ve had in the past with the output of pkg-config being encoded or interpreted wrong, given the strange @ symbols everywhere (which looks like some kind of 4-byte character encoding, maybe UTF-32). But given that you needed to modify the python encode/decode lines, I’m guessing you’ll be running python version 2.6? Python needs to be version 2.7 or above to work, as far as I can remember. And these encode/decode lines may very well have influenced this.
But given that you can run the code manually, you might get away with simply bypassing the pkg-config auto-detection, like this:
$ export EIGEN_CFLAGS="-isystem /usr/include/eigen3"
$ ./configure
If that doesn’t work, and you have a more up to date version of python installed (it’s just not the default), then you can invoke the relevant python executable with the script as an argument, like so:
python3 ./configure
python3 ./build
Hopefully one of these options will help…