When HSE firmware is not installed, SWD/JTAG access on the S32K3 can be restricted using the CUST_DB_PSWD_A field and device lifecycle configuration. Would enabling this password protection have any impact on performing an ARINC 615A software data load to the processor, assuming the update is handled by application or bootloader software rather than through the debug interface?
CUST_DB_PSWD_A only restricts SWD/JTAG debug access. I am not familiar with the details of your ARINC 615A implementation, but if the software load is handled entirely by your application or bootloader, I would not expect the debug password itself to have any impact.
Ultimately, this is application-specific and depends on how ARINC 615A has been implemented in your system. If the update mechanism does not use the debug interface, debug access restrictions should generally be independent of the software loading process. Any additional limitations would depend on your lifecycle configuration and application security design.