That's pretty much what I think but I think they need to clarify their clarification
The text is a little misleading.
I had a similar situation happen last night, and had to scour this forum to find the answer. Just now I checked the French rules and found that there would have been no question if they had translated it correctly. Neither the French nor German rules say "at the begining of his turn" under Yin Phase Step 2. It simply says (rough translation):
Step 2. Board overrun?
If the three locations of the board are occupied by ghosts, the player loses 1 Qi and does not perform step 3 (he does not add a ghost and goes directly to the Yang Phase).