The issue is that the OS now provides a convenient “backdoor” for root-privileged malware to capture sensitive data from any app effortlessly; it just needs to subscribe to file system events (using inotify) to grab the files as soon as they’re written. Without it, the malware developer would have to write hooks for each app they wanted to eavesdrop on individually, which raises the bar at least a little bit.
[1] https://www.kernel.org/doc/html/v4.18/filesystems/fscrypt.ht...
From a purely kernel perspective: it has been some time since I last looked at the kernel fs/dentry code, but from what I remember, the open file handle would hold refs for dentries that comprise the path [all the way up to mount root]. But even that wouldn't prevent other dentries from being cleared anyhow: only the open file would have unencrypted pages in the page cache. I would highly recommend reading the linux fscrypt code if you would like more details: it's very well structured and quite easy to get into!
Of course, the foolproof way would be to check lsof and nuke all processes that still have file handles open before logging out, but that's probably too much heresy :)