I don't recall the time period for the Summoners original existence, but it was likely while the ability to summon the primals was sealed at Silvertear Falls. I think this is the only seal you can put on them, that they can't be properly summoned, but their calmer, smaller representatives can. So, having the big manifestation trapped and locked in the Ultima Weapon/Silvertear Falls doesn't seem to keep the less willful versions from manifesting.