Perhaps, but I was explicitly told that the spots are not part of the D. The D is the lines (and arc). The spots are separate from the D and on club tables the spots may be outside of the D. The rule you quote only talks about the lines, not the spots.Of course referees must not rely on vague memories when written rules are available. Here is the pertinent section for snooker:
5. Playing from In-hand To play from in-hand, the cue-ball must be contacted by the tip of the cue from a position on or within the lines of the “D”, but it may be played in any direction. (a) The referee will state, if asked, whether the cue-ball is properly placed (that is, not outside the lines of the “D”)....This means that if the cue-ball is exactly on a line of the D, it is deemed to be legally placed. Further, if the cue-ball is exactly on the yellow or green spot, it is placed legally for playing from in-hand.
It seems that the referee training mentioned above was contrary to this part of the rules.
All that said, it is clear from the overhead camera that the cue ball was placed outside of the D and the foul was called correctly. Not sure if it should have been a miss as well....