This is a ketiv-qere phenomenon, that is, one reads the word differently from the way one spells it. The four letters are those of the tetragrammaton, which is never pronounced today. The vowels correspond to the word that is said euphemistically instead:
אֲדֹנָי→יְהֹוָה (equivalent to אְדֹנָי in Masoretic Hebrew, see my answer here)
This particular ketiv-qere is assumed everywhere due to its frequency. The same can be said for הִוא which is pointed (and read) as הִיא, or יְרוּשָׁלַ͏ִם for יְרוּשָׁלַיִם.
The original vowels of the tetragrammaton are not those of the Masoretic text.
The cholem-free form should be seen as a simple variant of יְהֹוָה which was accepted during Masoretic times. Since it is clear what is meant by יְהוָה it was sometimes used. I am unaware of any ancient treatise that makes any distinction between the two forms.