You could do something like this extremely hacky, quickly thrown together bash script as root on your system:
#!/bin/bash
for i in $(diff -qNur --no-dereference /usr/etc/ /etc/ &>/dev/null | grep "differ" | cut -d" " -f4 | grep etc | sort -u); do
rpm -qf "$i" | grep -v "not owned" >> /tmp/etc-owners.txt;
done;
sort -u /tmp/etc-owners.txt;
As always, don’t run random scripts from the Internet without understanding what they do.
I’m sure the script can be implemented much better, but it is probably mostly fine — and it works here — but it makes some wild assumptions, such as files not having spaces and currently having packages installed for the various files. It also will definitely show you files owned by packages that are part of Silverblue itself, so don’t try to remove everything that has a file changed.
It also doesn’t directly answer your question, nor does it show you orphaned files… but might point you in the right direction to know what currently-installed software has modified files.
If you cross-reference the output with rpm-ostree status, you can probably tell where many of the changes come from.
Edit: Actually, the first part of the command is probably even more useful, as it shows you the files that differ:
diff -qNur --no-dereference /usr/etc/ /etc/ 2>/dev/null
The paths and filenames are probably useful enough to indicate what they do.