The comment should say "you can only mount it once". It has nothing to do with subsites. I guess whoever the aD person was who wrote it was thinking that typically multi-mounted packages would be under different subsites, but there's no such restriction.
As for changing singleton_p false, just edit the .info file. Upgrading would involve whacking the value in apm_package_types. To make upgrading work properly you need to bump the version number by editing the .info file and by adding upgrade-old-new.sql files that correspond to the old and new version number.
Mind my asking which package you're changing?
