I think you have run into the same issue I recently did. I have purchased four TX3 mini boxes (2G/16G) over time from different vendors. Two of the boxes work perfectly (i.e. I can install to the built in eMMC. However on the other two boxes, I can not. The two boxes that can't install to eMMC, do work in all other ways. So I can run armbian from the SD card if I want.
In attempting to diagnose the problem, I noticed that the kernel wasn't detecting the internal storage at boot time. So I opened up the cases of a box that worked and a box that didn't and discovered a difference. The two boxes have different storage chips (the chips are actually located in different locations on the board as well). In googling the part markings on the chips, it appears that the box that works correctly has an eMMC memory chip installed, and the box that doesn't has a NAND chip installed. I recall reading somewhere that there isn't currently support in these kernels for nand storage. So it would seem that some manufacturers in order to cut costs are installing nand storage on some of the TX3 mini's. I don't know how to tell at ordering time, what type of storage might be used and therefore I no longer am purchasing the TX3 mini's for my purposes. I really like the boxes and if I could be assured of getting boxes with eMMC I would use them for a number of projects.