Hi Tim,
Although the NMI function on PTA4 can be disabled by clear the FTFA_FOPT[NMI_DIS]. The associated pin continues to default to NMI pin controls with internal pullup enabled. You still need to turn off the pullup when configuring the I/O port after RESET.

I am afraid you can't achieve that by software.
Have you ever considered add external pull-up resistors at all these pins?
Or don't use PTA4 pin.
Best Regards,
Robin