If I submit ten copies of the same game with different background colors, then all of them would get the same rating, because all of them provide the same value/quality. If the game's not poor, it will not get a poor rating.
Nonetheless, Apple would (rightly) want to ensure that this doesn't happen, since all the duplicates provide negative value, crowding out the competition, harming discoverability. On their own each of them would provide value, the problem is in duplication.
Allow ”hidden” apps which could be only found via direct link.
For the legitimate template apps described in article this should be ok as users are likely dedicated and can find the link to app for example via website.
Apple wants to have absolute control of what users are allowed to install on their own devices. Maybe that's justifiable as a way to avoid malware, and maybe it's also reasonable to extend the "evilness" check to cover apps which would drain the battery or interfere with other apps.
Apple also entirely reasonably wants quality control on what apps they're willing to advertise on their "store front".
But I think there's no justification for using the "store front" quality bar to block what users are allowed to install. If an individual or organisation is willing to pay to have an app developed for their own customers/staff/associates/family/whatever, Apple shouldn't be applying more than the "evilness" check before they permit people to install it.
(Alternatively Apple could agree to sign apps which pass the "evilness check" without hosting them, but they'd probably want to be able to remove them if they spot malware later rather than relying on some kind of certificate revocation. They could charge a reasonable fee to cover review and hosting costs.)
Nonetheless, Apple would (rightly) want to ensure that this doesn't happen, since all the duplicates provide negative value, crowding out the competition, harming discoverability. On their own each of them would provide value, the problem is in duplication.