Normally I use command line and only use JetPack for extra packages (I have an old tiny laptop with dual atom using Ubuntu, but my host I really work on is Fedora). What you need to know though is that each device being changed/added/removed from the carrier implies a device tree change is required. The original device tree won’t know about the “extra” network device. Regardless, JetPack is just a front end to command line anyway and the end result of command line flash should be no different than having JetPack run command line for you.
You mentioned PCI…is this new device on the PCI bus? Then this would require a kernel driver unless the driver is already there (which is quite possible if you used a popular chipset). On the other hand, if it uses a power rail from the Jetson, then the device tree would need to change for the power rail. If there is some need for the device at some particular stage of boot, then this too might require device tree changes (or even U-Boot changes). Some PCIe devices (namely FPGAs) might be require a delay before booting.
I can’t help much with custom boards, but whoever does help will need to know the specific details of how the device is connected, what driver it would use (or what chipset it is), at which point you need it in boot (e.g., if it can wait till the system is up versus if it is needed as a boot device), and how your carrier board differs (even slight differences are important). Any changes to kernel or device tree are important.
As similar as a TX2i and TX2 are their device tree will differ, so I don’t know if this is why the TX2i worked but the TX2 did not. Maybe the timing of some setup or default kernel config is the reason it worked.
Just something to consider…a full sized PC has a BIOS, and the BIOS acts to announce hardware and acts to set up basic operation (such as clocks and power rails) before the bootloader ever runs. An embedded system has none of that, and so you have to more or less manually account for this. The device tree (along with a more customized bootloader) is normally the method of doing this.