Ah, I did do a search but didn't see other posts for some reason. The interesting thing is that I only have this issue on my work computer, which is running Windows 10 Pro. On my personal computer, which is running plain Windows 10, the Windows Defender checkbox has always been selected but I've never seen the notification mentioned in my original post.
On Windows 10 Pro, I kept getting a message in the notification center that "Windows Defender needs to scan your computer" even though it runs automatically. After some digging, I found this reddit thread that had the solution: disabling the Windows Defender checkbox in CCleaner. One user suggested CCleaner might be deleting a log file that tells Windows Defender when it last did a scan. I did that and no longer receive the notification, so the CCleaner team might want to fix this behavior going forward.