Hello @ykarata1 ,
Currently, the MBDT toolbox provides only two ways of flashing the MBDT generated code: OpenSDA and Serial. The Serial represents the less expensive method to flash the board on your custom code. Because on the custom code, you will only place a header that connects to the UART signals (RX and TX) and the reset signal. The USB to Serial chip can be placed on another board.
The first scenario you proposed, where a third option should be available in our toolbox (JTAG), is not currently available. So you cannot flash directly from our toolbox via JTAG/SWD protocol. I think you can open a request for that.
The second scenario you proposed, requires to flash the generated code (elf file) using S32 Design Studio on your custom board. Any JTAG tool that appears in the drop-down list from the S32DS should do the job.

Just to give you a name, we use the Multilink probes. http://www.pemicro.com/products/product_viewDetails.cfm?product_id=15320168&productTab=1
Another way is to use an S32K144 EVB's OpenSDA as a debugger, via the SWD protocol. There is a header on the board that allows you to connect to an external MCU. We had an interesting discussion here last year, where one of our customers used an S32K144EVB board to flash his own custom PCB, https://community.nxp.com/t5/NXP-Model-Based-Design-Tools/Model-Based-Design-Tool-on-custom-pcb/m-p/...
Hope this helps,
Marius