Hi,
I have tested the lpuart_echo_s32k144 demo from SDK RTM 2.0.0 and see no issue, rx callback is called only once when byte is received.
Generally, you need not to clear any flags in callback functions. This callback is called from the interrupt handler which contains code for flags clearing already. Moreover RDRF flag is cleared by reading data register, so flag should be cleared before callback is called.
BR, Petr