I swore I fixed that typo before posting! XP
The "flaw" being human ambition. My headcanon for post-Calamity Allag is that they went the way of many a doomed precusor civilization and decided it was their duty to correct the inborn flaws of humanity to prevent another disaster. By, you know, tampering with the source code for the sake of genetically lobotomizing the species. As long as they don't do it for Evil™, it's fine right?
Except instead of learning humility and peaceful coexistence by being cut off from the works of their ancestors, this new race had perhaps the largest chip on its shoulder the world would ever see, and a whole lot to prove.
It means the Triad (specifically Sephirot) couldn't have been harnessed to augment Xande if they were captured after his resurrection. It may have been used for others later, but the Embiggening of Xande was an Amon original and took place before his Pokemon Journey.