When you look at the member list you'll notice under your name it'll say Square-Enix account with their logo and with the user name you made instead of the OIFOS235908 whatever POL ID we're all familiar with.
All I had to do was go into the login settings and remove the SE account user name and keep the one-time password to Do Not Use. Also it's important to keep your original POL password to saved since when active your SE account info overwrites the need for it. It won't let you leave your POL password unsaved.
Ninja edit: Tried logging in the old fashioned way. You were right, it requires the SE account info even when you disable it under POL settings. This is probably just a bug SE didn't foresee. Be sure to tell POL about it and I'm sure it will be patched up relatively soon. Your account is still "active" and that's all that matters.