I managed to find a work around.
In the following folder...
C:\MATLABAddOns\Toolboxes\NXP_MBDToolbox_S32K1xx\mbdtbx_s32k\mscripts\fcan
I made a copy of 'mbd_s32k_fcan_receive.p' and renamed the copy to 'mbd_s32k_fcan_receive_init.p' as shown in the screenshot below...

This appears to have fixed the problem, including the the bug with the extended CAN ID.
The patch to fix the extended CAN ID seems to change the function call in the the mask base of the FCAN receive block.
Before the patch, the initialization tab calls the function 'mbd_s32k_fcan_receive'.
After the patch, the initialization tab calls the function 'mbd_s32k_fcan_receive_init' (when MATLAB has been restarted after installing the patch).
What I dont know is if there is a difference between the two functions ''mbd_s32k_fcan_receive' and 'mbd_s32k_fcan_receive_init' ?
Because the 'mbd_s32k_fcan_receive_init' file is not included in the patch.