Nope, it's always been a binary (that I know of). However, if you open the exe file with Ubuntu/Debian's "Archive Manager", you should find all the individual files, including the perl script (named pullautin.pl - the main.pl is just a launcher script).
Note that it requires several perl modules, notably libconfig-tiny-perl and libgd-perl on Ubuntu/Debian, as well as Geo::ShapeFile which can be installed with CPAN (see https://metacpan.org/pod/Geo%3a%3aShapeFile
Plus, you'll have to modify the perl script. I do have a linux version of it here, but I'm hesitant to post it publicly as the license is unclear on redistribution. Basically, it involves changing the paths (forward/backward slashes), plus change all references to pullauta to the name of the script (ie puallautin.pl) (this is when it's called recursively, as you figured out).