If PADI received complaints or concerns about the training being done, which is what is implied in the letter at the top of the thread, they MUST look into it. Likely they found training was not meeting their standards, or perhaps they received multiple complaints that were not published here. Dive shops must meet certain standards, are subject to audits, must jump through many hoops and probably pay for the right to REPRESENT the organization and use the PADI name for profit. PADI reserves the right to choose who represents them and their $$$ name. We may never know the whole story.
As for filling tanks at non PADI shops, of course PADI would rather you give your $$ to a shop bearing their name, but as long as the fills are done properly and to spec, it doesn't matter.