I think the PUA version are just potentially unwanted things that exhibit trojan-like behavior but aren't confirmed trojans.
As for the original question, it looks like it's only using the first part of that to determine the group of PUAs to ignore.
These are the 'PUA' families (and associated signature counts).
82 Andr
181 Cert
4 Doc
2 Email
1 Embedded
34 Html
3 Java
2 Js
1 Osx
1 Packed
6 Pdf
1 Php
1 Rtf
1 Spy
1 Swf
1 Tool
542 Unix
5832 Win
Running clamscan --detect-pua=yes --exclude-pua=Pdf does indeed exclude the 6 PUA signatures for PUA.Pdf.*
Barring the addition of functionality to allow you specify sub-categories on the command line, your best option would be to create a .ign2 file with a list of all the packer signatures you want to ignore.
A command-line along the lines of this would generate it for you:
# sigtool --find-sigs PUA.Win.Packer | awk '/ PUA/ { print $NF } /:PUA/ { print $NF }' | awk -F: '$1 ~ /PUA/ { print $1 } $NF ~ /PUA/ { print $NF }' | awk -F\; '{ print $1 }' ><dbdir>/ignorelist.ign2
--Maarten