Well, we've already learned from "Code = Boro > Delta" that Boruto's statemente are a bit contradictory. I don't remember exactly what the current scale is in relation to Jigen and Code, but perhaps we could simply consider Unlimited Code > Jigen without the Juubi chakra?
Because Jigen went after the Juubi and took chakra, immediately went to his second form, and then he went to the village. He didn't want to fight, but he knew it might be inevitable, so he strengthened himself beforehand. This can be supported by Kawaki's statement that Jigen might be inferior to Naruto, since Kawaki only knew Jigen without the Juubi's chakra, since Naruto and Sasuke could keep up with Jigen v1, and Jigen's physical blows only caused them pain, but not enough to take them out of combat. Basically: Isshiki > Jigen v2 enhanced by the Juubi > Jigen v1 enhanced by the Juubi ≥ Naruto Rikudo ≥ Unlimited Code > "Standard" Jigen v2 > "Standard" Jigen v1. It's worth remembering that Amado and Code mention they had doubts about whether the limited Code could defeat a weakened Naruto and Sasuke; it wouldn't be absurd for him unlimited to lose to one of them at their peak or be on the same level. Also, Jigen couldn't withstand Isshiki's full power, right? It's possible that Isshiki in Jigen's body is also weakened and far inferior to Jigen in his original body.