First do this:
set QT extra args to your prefered dir (QT_EXTRA_ARGS=--prefix=$HOME/kobo/qt),
then use this command: export PKG_CONFIG_PATH=/home/<USER_DIR>/kobo/fs/lib/pkgconfig <== make sure this path exists!!
test if you run this:
you get no input files (not: command not found)
and then try it again.
Let me know if this was the solution!
P.S. I need to run build-all.sh as root because at the end 'make' needs access to a root dir. I don' t know if that is neccesary for you, but for me I needed to compile qt again (which took me about 3 hours