Hi Andrew,
you can use PE micro debug server and client directly. pegdbserver_console.exe is located in
[YOUR_S32DS_INSTALL_PATH]\S32DS_ARM_v2018.R1/eclipse/plugins/com.pemicro.debug.gdbjtag.pne_3.6.5.201808141630/win32

and use gdb client arm-none-eabi-gdb.exe located in
[YOUR_S32DS_INSTALL_PATH]\S32DS_ARM_v2018.R1\Cross_Tools\gcc-arm-none-eabi-4_9\bin\

You can add your commands into file - in my case my_commands.txt which contains (attached for reference):
target remote localhost:7224
load c:/nxp/hello_world_s32k144.elf
This flashes hello_world_s32k144.elf into board. You can find more gdb client commands with help command:

Hope it helps.
Jiri