Just a bit of knowledge for those who were interested:
You can place any files you want to copy to the wii u (rom.zip, meta files, etc.) onto the SD card. From there you can use the mount_sd() command to mount it from wupclient, and then you can use the w.cp command to copy a single file from SD to NAND/USB, something like this:
w.cp("/vol/storage_sdcard/rom.zip", "/vol/storage_usb01/usr/title/00050000/10179B00/content/0010/rom.zip")
Another thing you could do is place any meta files you want to change for a VC game, and then use the w.cpdir command to move them all at once:
w.cpdir("/vol/storage_sdcard/meta", "/vol/storage_usb01/usr/title/00050000/10179B00/meta")
That's a much faster way to copy over modified meta files.
Edit: Also the same thing can be done in reverse to dump files faster than doing so over the network.
Also looking into it, you can use the same technique to dump a 1:1 decrypted (loadiine-ready) copy of a game if you use mount_odd_content() and then w.cpdir from /vol/storage_odd_content to SD. Not of much use now, but for games that are disc only it would allow us to dump the game, encrypt it to install-ready files using other software, and then with a forged ticket install to sig-patched redNAND