yep, rsync is not used but before tree sync happens, cache is generated for entire tree. each time. and users getting the cache. Its not a problem. A problem could be that cache is wrong. Need to check this. To verify my idea, what you could is (and report results)
rm -rf /usr/portage
emerge --sync
du -sh /usr/portage/metadata/md5-cache
mv /usr/portage/metadata/md5-cache /tmp
egencache --update --repo=gentoo --jobs=X (where X is your CPU naumber)
du -sh /usr/portage/metadata/md5-cache
also you can do a diff between qt-creater, freshly generated and the one from /tmp/md5-cache (moved from vanilla tree), See if this differs