Yes, erased Android from the eMMC. Keep in mind this erases all data, apps and user data. Note, I was unable to erase eMMC using the keys method, I used the interrupt method. With the eMMC erased, the VIM3 will not boot from eMMC, as no OS is present.
You can leave the eMMC empty if you intend to run from card.
If you want Ubuntu on the eMMC, and you want to use an image with the latest(Khadas) Linux kernel(5.*), looks like using the SD card image is the only option right now.
If you are OK using another kernel(4.9), other methods exist to burn the image to emmc, such as the USB Burning Tool. I believe it is possible to install Linux to eMMC from the Khadas SD/USB images. I have not done this with the Khadas images myself so I cannot offer tips. I will try it tonight and report back.
Khadas Team member @hyphop offers an excellent tiny OS called Krescue. Krescue is run from SD card and can be used to install OS images to eMMC. He offers several Krescue Ubuntu images that can be used by Krescue to burn the image to the eMMC. See Krescue README here. Krescue install and images are a work-in-progess, so some bugs might be expected.
User @balbes150 offers some excellent Linux options that can be run from SD card, also can be installed to eMMC using a script.
This is much information to digest, fell free to ask any question you have about any of it.