I sorta believe the fountain's plumbing was left there just under the floor..... Disney does not usually rip out stuff unless it has to.....for example areas of showbuildings not used by the "new ride" still having the old areas with stuff from the old still in the areas out of sight.... in this case the plumbing probably still exists in the Utilidor area beneath the Tiki Room.... will it need updating (the plumbing)??? Probably....
I also agree that the permit is likely part of a more general permit... perhaps seek out permits for areas within the Utilidors themselves.....would be a "cute" way to mask their true purpose!
Of course this is all pure guess work....especially if the over riding rumors are untrue then there would be no fountain.
I Love the Enchanted Fountain.....
when we were at Disneyland last year I really enjoyed just watching it flow before the show began...I had forgotten how truly beautiful it was!