Do you have to look away from the road every time you push the blinker stalk? Do you accidently flash incoming traffic everytime it starts to rain? There's a lot of things you already have to do in a car at once. Operate at least two pedals, a steering wheel, a few stalks and buttons, observe and obey traffic signage, observe and predict the actions of other drivers, navigate, deal with passengers, adapt to road conditions, etc. There's so much to think about, and frankly operating a clutch and stick is easier to do than a lot of these individually.

The other day I was at an intersection; the car in front of me went, and my mind focused on the shifting for a moment - my brain decided to put the driving on 'autopilot' instead of the shifting. In that brief moment, when I was more focused on shifting than the road situation, I nearly drove out in front of an oncoming vehicle. Had they not honked I may have failed to notice until a collision occurred.

Clearly it's not second nature yet. Keep practicing. I know that feeling you're talking about, that draw of focus. It's not your brain picking a new focus willy-nilly - it's a lapse in your shifting muscle memory, forcing you to engage more consciously. I get that feeling every time I get a car new to me, manual or not. You just have to learn it.

Hell, I've been driving manuals for pretty much my whole life, and I can share counter-anecdotes of me having similar lapses when I had to drive an auto. Last time I did, I slammed my left foot into the brake pedal to instinctively press the clutch that wasn't there, and was momentarily distracted from the road when I tried to shift into low with the wiper stalk (mountain road). And this was a car that I had daylied years prior. You just need to get familiar with your car. Practice practice.