Sorry for the slow reply. I was off for a while around the holidays.
The modifySql doesn't try to be smart at all, it just does a simple text replacement like you noticed. The simplest approach is probably to use the regexp tag or the replace tag to replace the end of the "create table" statement.
Alternately, you could create an extension (liquibase.org/extensions) that overrides the CreateTableGenerator to add on the partition information on non-XE databases without needing to add anything into the xml file.
Nathan