I have replaced the default HAL time code with a 32768 Hz timer - that’s the frequency MCCI LMIC uses by default.
See the post A fork to add SAMD21 standby support to LMIC
The timer initialisation code won’t help you, but you should be able to get the idea - initialise a timer at the correct frequency and make a couple of other changes.
It seems to work well.
Regards, David.