I would guess that many early systems just didn't have the storage space for a lot of multiple versions of files. Was VMS saving diffs or full copies of files?

Once storage space was plentiful, the pattern of "overwrite the existing file" was already well established.

Typical TOPS-20 and VMS hardware of the time would have less than a gigabyte of spinning disk space, to be shared among many dozens of users. Full copies of files were saved, and there were strict per-user disk allotments. Creating Generation 2 of a file would mark the Generation 1 version as deleted. When you ran out of allotment during execution, the OS would pause your program and give you the chance to issue an Expunge command to really recycle all (or a subset) of the deleted files, and then you'd just Continue the paused process. Similar to desktop "Trash" folders where deleted things go, and that you may have to Empty once in a while.