It has been more than a year now, and this still has not been resolved. My US LLC Apple Developer account is still stuck in limbo. Apple has not given me any response. They just don't care. During this time, I used a friend's developer account to sign my Mac app and distribute it on my own website. I was not trying to ship on the App Store anyway. Later, I enrolled as an individual and published an iOS app under that account. After that, my personal account could also sign and notarize my Mac app normally. But I still want my US LLC developer account back. I do not want to publish Mac or iOS apps under my personal developer account. These are commercial products, and I think it is better to ship them under a company entity. My original hope was that after the membership expired for a year, I could re-enroll and the account would return to a normal state. But that did not happen. Even though the membership has expired, Apple still will not let me enroll again. The page still says: Sorry, you can't enroll at this time. Your Apple Account is already associated with the Account Holder of a membership. Apple is a big company. They just don't care. They refuse to tell you any reason, and it does not look like they want to solve this problem at all.

I encountered the exact same issue as you. Nov 14: Registered an Apple developer account for my US company Nov 16: Received an email requesting additional documents Nov 17: Submitted documents Nov 19: Received email: Your enrollment is currently under review Nov 22, 8 AM: Received email: Your enrollment request has been accepted. Clicked link to continue application process, successfully paid $99. Nov 22, 4 PM: Received email: Welcome to the Apple Developer Program. Passed review. Can see organization information when logging into Apple developer website. Nov 28: Created a certificate on Developer website, signed and notarized my Mac App (developed using Electron), notarization remained in "In Progress" status. Nov 30: Checked notarization status, changed to "Rejected". Checked certificate status, found certificate had been revoked. Opened Apple developer website, organization information disappeared. Only an Enroll button remained. Clicking it resulted in error: Your Apple ID is already associated with the Account Holder of a membership. I can see my organization information in App Store Connect, I am the Account Holder of this organization. From November 30 to December 12, I sent 2 emails and made 4 phone calls to Apple support. They only told me that there is a support ticket for my issue, but it's still in pending status, with no additional information available. I don't need to do anything. Just wait. I don't know what I did to trigger this issue. Apple support hasn't provided any useful information either.