Can I control a Microchip USB3300 Transceiver with a USB 1.1 host controller IP?
No, that won't work at all. The IP core you're looking at was designed to operate with a USB 1.1 tranceiver like the Fairchild USB1T11A, which is little more than a differential driver/receiver. A USB 2.0 transceiver like the Microchip USB3300 is a wholly different device -- it performs high-speed de/serialization and presents an 8-bit parallel interface.