Hmmmm. Good question.
The software I mention does only one thing, and that is to "permanently borrow" (or clone/steal, if you prefer). It's just a quicker easier way to the previously used "delete/reload game updates method"
But since all that is changed in your save file is a "flag" which determines whether a car is "owned" or "borrowed", I would say there is nothing to worry about.
Technically, yes you are altering your gamesave, but by such a minute amount that I really doubt PD would bother chasing you. They have many more bigger issues to deal with recently.