It is how the two commands have always worked and why when you use the
Save As command you are prompted if the file already exists as to
whether or not you want to replace the existing one.
The Save command only saves the changes to the file and saves them in
the next available place large enough for the fragment. That can be
anywhere on the drive. The file manager then records a link and the
next time the file is read into memory the file system follows the links
until all of the file is in memory. That's what causes the heads to
sometimes skip all over the place when loading the file and why it takes
a long time and a lot of disk activity to load some files.
If the file is a series of fragments scattered all over the drive then
selecting Save As will write a new, contiguous copy in a location that
can hold it, thus eliminating the need for links. The file manager then
marks the old pieces as available and the next defrag will consolidate
these pieces of free space into larger contiguous areas available for
writes. In the meantime disk performance improves because the drive
heads are moving far less, shortening access time and reducing wear and
tear. There is no downside that I know of to using Save As except the
additional step of confirming the "overwrite". No overwrite takes
place, of course, since it is a new write. "Overwrite" is just an
anecdotal descriptor for what really happens.
This is a very old computer tip that is still valid. If you search the
web though you will see explanations of the difference between the two
commands as simply being that Save As offers the opportunity to create a
new copy while keeping the old one by changing the file name. That is
one of the reasons to sometimes use Save As but by no means the most
useful IMHO.
It is understanding what the Save command does NOT do that is the key.
It does not save the entire file, but only the changes from the current
session. These are not written into the existing file but in a new
location large enough to hold the changes.