ISE,
There's a bug in Autotune where it correctly states that those fields should be blank, but it's not able to clear them. We're working on a v5.1.1 release which will fix this and a few other minor issues.
To remove those fields in the Facebook Developers area, you should click the 'X' in the top right corner of the 'App on Facebook' and 'Page Tab' sections, then click save. Removing those settings is not critical in any way. Autotune has simply been improved in this version to not enable features that your Application can't use (those features require SSL, and your site was automatically detected to not have it enabled).
I hope that helps explain, and sorry for the minor bug.
Alex