The most important thing to realize about the “file system” in Linux is it does a lot more than just persist your documents and app data. You shouldn’t index your root directory because almost everything other than your home directory is some kind of Linux distro/application-specific directory that is often not a normal directory stored on a storage device. If you run the mount command with no arguments, every line of output is a separate file system, mounted at some specific directory of the current “mount namespace”. Kinda confusing, but every process in Linux has a mount namespace that has a list of mounted file systems, often that namespace is shared between many/most processes, such as your terminal shell. Most of the file systems will be virtual i.e. not representing anything in storage. For example sysfs (always mounted at /sys), proc (always mounted at /proc), devtmpfs (mounted at /dev), etc. are all completely virtual and are ways for system services and applications to access state and devices exposed by the Linux kernel. They should never be indexed, treated as normal files, or modified by the user.
That’s probably even more confusing, sorry. But the gist of it is, the only directory on your system you can really count on actually being stored on disk and always available to you is your home directory. Basically everything else exists as an implementation detail of the operating system and software applications.
If I were you, I’d stick to only indexing your user home directory. Indexing /usr or /tmp or /etc or whatever is like indexing C:\Windows and C:\Program Files, except even weirder since at least on Windows those are actually files stored on disk whereas in Linux they may not even be actual files (although most of them in /usr and /etc are actual files on disk).