A Chinese ST-Link dongle costs about $3. You can connect it to the SWD header on a Due board but the Dupont cables get in the way of a shield.
Rowley is perfectly happy with using an ST-Link with a non-ST Target.
Keil should be happy too.
Of course Atmel Studio only supports CMSIS-DAP or JLink debugger with its proprietary chips.
You can install JLink firmware into a ST-Link dongle but Segger do not allow you to use non-ST targets.
If you use the JTAG header on Due or M0 boards the JTAG ribbon does not interfere with shields.
You need to buy a 1.27mm pitch 5x2 cable and adapter board which is as expensive as the ST-Link dongle. e.g.
adapter + cablesI believe that NXP evaluation boards have got CMSIS-DAP debugger and 1.27mm pitch 5x2 header. So you only need the ribbon cable.
In theory, the Microchip SNAP is both cheap and can do SWD debugging.
Regarding EDBG using a UC32 chip. ST use their STM32F103. NXP use their LPC. Freescale used their K20. ...
I would guess that any reasonably powerful chip could run the CMSIS-DAP firmware.
You would certainly AVOID using the mEDBG mega32U4. It is too painful.
David.