As far as I know, ... maybe. There's some conflicting documentation on whether a different bootcode.bin is needed for eMMC boot compared to SD boot. If it is, you'd need to modify the OS image and replace the bootloader before "flashing" it into the eMMC.For the OS, would a standard linux distro boot on the board, allowing kernel/driver patching & compiling 'in-situ'.
Well, the Broadcom SoC AFAIK doesn't have Ethernet built in, so I'm assuming you mean the RST from LAN9514. The "config file" here would be a Device Tree file, https://github.com/raspberrypi/firmware/tree/master/boot , these are compiled binaries, an example of the source would be https://github.com/torvalds/linux/blob/master/arch/arm/boot/dts/bcm2835-rpi.dtsi (just a small part of the result, it's an "include" file, the official rpi binaries can be de-compiled and modified, which would be probably easier). My idea was to build the daughterboard like it was RPi3, so we could use the RPi3 device tree file without modification (with just an added overlay for the eMMC). Otherwise we would have to define most of the hardware manually (if we were to start with a CM3 device tree file).The must significant difference between the RPi3 and our streamer board (from an RPi software perspective) is that the GPIO pin used for Ethernet Reset has been moved to free up an I2C port, so Linux Config file (what ever its called) will need to be modified to reassign the GPIO used for the LAN Reset pin to the new I/O port pin.
The syntax looks easy (and is documented), but it's really not, at least not for a regular sysadmin like me, the pin definitions and addresses and aliases and interrupt controllers are all over the place. But it's an "open" and documented format, so somebody should be able to reconfigure the Ethernet RST pin after some reading and trying. Then the modified version can be manually specified in config.txt (read by bootcode.bin) or through u-boot (or a different second (?) stage loader).