Hey, so Hawairish, I just stumbled on this thread and watched your videos. Here's my take on the issue. I don't think what you noticed has anything to do with the drive-by-wire system. It has everything to do with the torque converter and the insufficient low-range gearing of the stock transfer case. I don't know if you have the TX10 part time case or the TX14 full-time case, but neither t-rcase really has low-enough gearing for the kind of terrain and obstacles you are driving on. Before I installed my crawler gears into the TX10, I used two techniques to counter the poor performance in 4L on that type of terrain.
First, I used the e-brake engaged part-way. This allows for controlled crawling up and over an obstacle without the quick and potentially damaging drop afterwards as the suspension compresses. You essentially drive using only the gas pedal, fighting both the obstacle's and the e-brake's resistance to tire rotation. Another technique I use (and still do, even with the crawler gears) is left-foot braking. I try to apply firm, but light consistent pressure on the brake while finessing the gas pedal. Don't let the obstacle determine how smoothly you make it over, let your feet do the "walking".
That being said, if your off-roading will continue to involve obstacles such as the ones in your video, and you have the part-time transfer case, I would strongly recommend swapping out the 2.02:1 low-range gears for at least the 3.7:1 gears sold by 4x4parts.com. These totally transformed my enjoyment of rock-crawling over challenging terrain such as the stuff you're driving on. (Plus, they enabled me to actually crawl at high altitudes, where the 3.3L engine has only about 125HP.)