When updating packages, I no longer get the message that there are binary versions available but the source versions are later, with the option to compile from source. If the source is newer it just reinstalls the older binary with no warning message. This occurs on both of my Mac computers, one arm64 and one x86_64.
As is, I check for updates, update and then check for updates again. For any package that is still on the list I rerun install.packages() with type = "source" or just wait a day or two for new binaries to appear.