Hello,
I am not familiar with MBDT but I will explain how clocking works for eTimer.
eTimer is supplied by MOTC_CLK as reference manual states:

So for setting MOTC_CLK you need to configure Auxiliary Clock 0 Divider 0 Configuration Register
(MC_CGM_AC0_DC0):

And also you need to know clock supply for AUX0, this is defined by your setting of MC_CGM_AC0_SC

So configure divider of your MOTC_CLK according to your needs, this is your eTimer clock.
Best regards,
Peter