USB3.0 OTG SSTX/SSRX crossover confusion
In USB3, transmitter on one end of link must be connected to receiver on the other end of USB link segment. And vice versa. The fundamental flaw in your approach is that you are using non-standard (and USB-illegal) "USB3 Micro-B to Female-A OTG cable", and eventually made an illegal "Micro-B to Micro-B" cable. As you pointed yourself to the Toradex website, different people are crafting cables to their understanding or rather misunderstanding. 

From the Toradex site:


  In the USB 3.0 specifications, only the following cable assemblies are
  specified:
  
  USB 3.0 Standard-A to USB 3.0 Standard-B Cable (SuperSpeed RX and TX
  are crossed in the cable)
  
  USB 3.0 Standard-A to USB 3.0 Micro-B Cable (SuperSpeed RX and TX
  crossed in the cable)
  
  USB 3.0 Micro-A to USB 3.0 Micro-B Cable (SuperSpeed RX and TX crossed
  in the cable)
  
  USB 3.0 Micro-A to USB 3.0 Standard-B Cable (SuperSpeed RX and TX
  crossed in the cable)


The OTG cable is really standardized, but the standard condition for OTG port is to use micro-AB connector, which can mate with both micro-B (as for device mode) and with micro-A (for host mode). 

Note: in all legal cables the Rx and Tx pairs are crossed. Get the correct cable combination (preferably micro-A to Micro-B), and move on.