Personally I still don't trust Shopkeeper at all. Like even if Garden and WISE had a similar goal or motives he would not hesitate to exterminate them first chance he got. He seems to hate the west too much thanks to his loyalty to the dead empire.
It has made speculation about Garden and WISE teaming up very hard to accept for me. If anything he's going to be the one that tries to kidnap Anya since she's probably related to the royal line.