No, its in addition. There are micro-clean environments inside the tools themselves. The wafer chamber is a couple of orders of magnitude clean. The plastic box that carries 15-20 wafers has to be specially made for cleanliness, each piece costing thousands of dollars. Entegris makes these boxes too [1].

[1] https://www.entegris.com/shop/en/USD/Products/Wafer-Handling...