Are you seeing any latency or missed commands? If not, leave everything alone & don’t worry about the numbers.
ZHA & Z2M use different ways of calculating LQI, plus there have been reports that the ZBT-2 shows a lower LQI than the SkyConnect, even with the same Zigbee integration.
Just to rule out USB interference, make sure you’re using a USB2 port on the Pi4 & not the blue USB3 ones. USB3 causes interference in the 2.4G spectrum which zigbee uses.
Make sure the ZBT2 is as far away from the Pi as the cable allows.
Be extremely careful if you’re swapping your USB port connection from USB3 to USB2 - if you defined your adapter path using the device path instead of the serial path, you’ll have to change your Z2M config since device path changes when you change port.