Securing Linux should probably not be approached the exact same way as securing Windows. Case in point, it is true that I can't find all of the .so files that have been modified since my package manager installed them: this is because it didn't install them, because I am using NixOS. They just exist in the Nix store, which is mounted read-only, and almost all modules are loaded from an absolute runpath.
NixOS with impermanence isn't exactly a security solution, but it does have some nice properties as a base for a secure system. It's also far from the only or even most notable of the immutable Linux systems, with abroot and RPM-ostree seeing more usage. It's probable there will still be some use in endpoint security but I suspect it will be greatly diminished if immutable image-based deployments with a secure boot chain is perfected on the Linux desktop system, for similar reasons to why it isn't really as important on ChromeOS either.
I also understand that this is not a silver bullet, as it's still possible on desktop Linux to persist malware through the bashrc/etc. like this does. Personally I blank out my home directory shell profile files and keep them root-owned to try to prevent them from being used for anything. It seems like more work is needed in the Linux ecosystem to figure out what to do about attack vectors like these, though I think a proactive approach would be preferred. (Scanning for infected files is always going to be useful, but obviously it's better if you stop it from happening in the first place.) In some ways the Linux desktop has gotten a bit more secure but many things are still not sandboxed sufficiently, which is a shame considering all of the great sandboxing technology available on Linux.