If you say so...
The fact that many do it, doesn't make it legal. A lot of murders happen daily. Does that make them legal?
From what I remember, the wording in the law is a bit vague indeed, as it is not 100% clear that the "guide" or "supervisor" should be diving tοο. I'm not a lawyer to interpret Indonesian law. After all, everything is fine until sh*t hits the fan.
Back to the original question. One cannot expect that he/she will be allowed to do unguided dives everywhere in Indonesia. The law prohibits it and in practice a lot of places won't do it. A lot of other places do allow it (hopping for the best?), and some (see Indah at Divers Lodge Lembeh - I think I remember he wasn't allowing it in his other resorts) take the responsibility and provide shore "supervision".
That's all I have to say for this.