That is probably one of the major issues. Also, EL5 had some interesting problems in the x86_64 version with installing i386 packages as well. I don’t recall if that was intended behavior or an actual bug. Either way, based on the errors, that’s part of what’s causing some of the errors.
I have no idea if the official client will run on something with packages so old. Letsencrypt is packaged in EPEL for version 7, but nothing lower. It’s very likely that this is because of dependencies on packages newer than either system is packaging. The auto script works around this by making a virtualenv and installing some newer stuff locally.
The best bet is to first try to manually install the packages that the auto script is attempting. You can manage installation errors a bit better in that case, which will help.
If you’re running into too many issues, some of the community-contributed tools use a lot less dependencies (they manage a lot less) and are more likely to work on older systems.