For repoman checks, the profile referenced by /etc/portage/make.profile should be irrelevant if the ebuilds reside in a different checkout of the gentoo repo (for example repoman might be running in a git checkout while /etc/portage/make.profile refers to an rsync repo). Currently, Package instances are constructed using a RootConfig instance that references the RepoSettings.repoman_settings instance attribute, and this config instance refers to /etc/portage/make.profile. This causes IUSE.missing errors to use IUSE_IMPLICIT data from /etc/portage/make.profile rather than my git checkout.
repoman support has been removed per bug 835013. Please file a new bug (or, I suppose, reopen this one) if you feel this check is still applicable to pkgcheck and doesn't already exist.