Here's the schematic & layout, please create a version with the parts you are suggesting.
Top & bottom mount surface mount headers would be one way to keep the physical board the same size, as long as its cut back from the USB header.
I tried the TXB0108 and finally gave up.
The blue boxes in the attached picture contain 3 pcs pf TXB0108.
I made the beta board and tested it.
While I test the TXB0108 5V output with voltmeter, the voltage is 3V.
However, I test it with oscilloscope, the output is 5V. I touch the wire or chip with my finger, the voltage became unstable.
Well, I think, the TXB0108 is easy to go into self-excited oscillation process. And the load capacity is small. If I connect other devices to it through long cables, such as a digital sensor, the output may have problem. However, if I intert the sensor in the header of the beta DUE board directly, it works fine.
I tried many time but still didn't success.
Not sure if the TXB0108 performs not good enough.