Hello sparkee,
Well, constantinrazvan.chivu is right, the issue regarding the Recorder error will be investigated.
But, I understand from your post that there are actually two issues:
1. the connection through the multilink probe when the FreeMaster block is in the model.
How do you perform the settings for the Multilink probe in FreeMaster?
I tried going in the Options to the Comm options and selected in the Plug-In module the first option "FreeMASTER BDM Communication Plug-In"

Now, by pressing the Configure button, the following Window appears. Here I selected the P&E CortexM and selected the connection to USB Multilink. The only speed required here is the JTAG Clock Speed.

Using this setup, I was able to connect to the board even if the FreeMaster Config block is in the model so no changes had to be made in the model.
Instead of USB Multilink, you can select also the OpenSDA which comes directly on the S32K144 EVB but, if you are using the PEMicro, I suggest to power up the board externally in order to disconnect the OpenSDA from the circuit ( cheange the J107 to other position and unplug the USB cable). If not, then there will be two debuggers (Multilink and OpenSDA on the same JTAG link to the controller).

2. The problem with the recorder. Well, you have a compile issue but I tried to use the recorder using this setup and I got the following message error: Recorder could not be initialised. Error 0x80000081 (Invalid command.)

Once again, I will ask our friend iulianstan to help us answer this question: Is the FreeMaster Recoder available over the Jtag connection?
Hope this helps,
Marius