/usr/local is for files that do not originate from the distribution /
vendor.
It is a place users put stuff. /usr/local absolutely must not be merged
with /usr.
Keeping the directories separate can prevent system / distribution files
from being overwritten.
Deleting files from /usr/local is simple. Restoring files from /usr/, or
figuring out which files in there
are from the distribution and which ones are not, is not.

Additionally, there are some other benefits to /usr/local/. For example,
you could put /usr/local/bin/ in PATH first for users, so they
preferredly get your desired custom version of a binary.
And you can exclud it from PATH, or place it last, if you are root, and
want to prefer the trusted binaries from the distribution, or only use
those. In this sense, it can even act as a security boundary.