@Xue Liu -X (xueliu3) Thanks for posting in our Q&A.
For this issue, I have manually installed the newest version (42.11.1) of this app in my iOS device which is not enrolled in intune. Microsoft 365 sign-in pop-up still exists.
Based on my understanding, intune doesn't control it.
Or please create an online support ticket to find something from intune backend. Here is the support link:
https://learn.microsoft.com/en-us/mem/get-support
Thanks for your understanding.
If the answer is the right solution, please click "Accept Answer" and kindly upvote it. If you have extra questions about this answer, please click "Comment".
Note: Please follow the steps in our documentation to enable e-mail notifications if you want to receive the related email notification for this thread.