Hi Kyf,
here are my answers:
1,2 : we are preparing S32K344 Motor control development kit. When the development kit hw is available you will find there also dedicated application note as well as sw example.
https://www.nxp.com/MCSPTE1AK344
3) Yes it is MCB mode with counting on external input (in our case external input on output from trigermux modul. Trigermux module in this way connects LCU and eMIOS). CW and CCW LCU outputs are connected to eMIOS. Picture you were referring to.

4) There are 2 eMIOS channels (cw and ccw) and their counters are set to increment only. Absolut position is obtained by subtraction absolute = cw - ccw. So absolute position is decremented when ccw is incremented. When motor is spinning in ccw direction cw value doesn't increase and similarly it works for cw direction. Absolute position is incremented or decremented based on speed direction.
5) ATO stands for angle tracking observer. I recommend to install AMMCLIB for S32K3
https://www.nxp.com/webapp/swlicensing/sso/downloadSoftware.sp?catid=SW32K3-MMCL1D
After installation you can find ATO description in
C:\NXP\AMMCLIB\S32K3xx_AMMCLIB_v1.1.29\doc\S32K3XXMCLUG.pdf
AMCLIB_TrackObsrv
6) Final rotor speed are stored to selected variables which addresses(pPosEst,pVelocityEst) are sent to AMCLIB_TrackObsrv.
void AMCLIB_TrackObsrv_FLT(tFloat fltPhaseErr, tFloat *pPosEst, tFloat *pVelocityEst, AMCLIB_TRACK_OBSRV_T_FLT *pCtrl);
Best regards,
Tomas Fedor.