Is there a way I can convert from USB to LVDS UART (~1Mbps)?
Typically an UART does not include a PHY, and thus any external PHY can be used for implementing the communication bus.
So feel free to select any suitable PHY for this, there are a lot of PHYs that implement low EMI by using a differential connection or limiting the slew rate. The PHYs include RS485, CAN, in addition to LVDS of course.