Will not start?

Okay, when you say the unit passed, does that mean the short was at fuse 11? And did you plug the other units back in before moving on to the next? The Black connector for smart entrance control unit is for all the door switches, hood switch, door lock actuators, anything that has to do with the security system, you can see some of the switches in the 1st diagram below, so the security system most likely rearmed when you plugged something back in. But that Black connector needs to be plugged back in. Is there an issue with the connector, is it disformed from getting hot or is there an issue with the unit it plugs into?

Here is all the information on the security system, without that connector plugged in the system is seeing all the doors open and setting the alarm off. On diagram 6 it shows how to deactivate the system, with Fuse 11 not supplying power though, you will just have to try locking and unlocking the vehicle or using the remote key fob.

The alarm won't disable until it sees all the doors closed. Are you sure there are no other blown fuses anywhere else in the vehicle? The alarm system is definitely preventing it from starting. But Fuse 11 feeds both the White and Black connectors of the smart entrance control unit.
If the test results mean there was still a short after unplugging the first 2 control units and the Black connector, then short from Fuse 11 is either through the White connector, in the wiring harness from the fuse panel, or the rear window defogger relay circuit. And moving the harness around when trying to disconnect those connectors can actually move the short away from the contact location. Did you also pull out the rear defrost relay as well?

If the harness is that tight, unbolting the module so you have more movement is a better idea, pulling on harnesses can cause pin fitment issues., But that fuse runs to those 3 units the rear defrost relay which is controlled by the smart entrance control unit, so it all comes back to that unit, or a harness issue. But it only takes a small section of wiring harness missing the insulation touching any metal section of frame or body too short to ground. Most shorts are so small you can barely see them, that's why I put a test light on the shorted circuit and watch the test light when moving the harness around, if that test light flickers the smallest bit, you know you're near the short to ground.
Here go through these couple videos, he uses a power probe 3 and show visually what you're looking for, it will help more than me just trying to explain everything. it will help with your testing too.

https://www.onallcylinders.com/2019/07/24/how-to-diagnose-electrical-ground-issues/