This all looks and sounds totally great! Couple answers to your questions:
Yes, it’s true that a three-note-per-string scale is going to require inside and outside picking no matter which pickstroke you start on. But that doesn’t mean both versions are the same thing. You didn’t learn a scale as a collection of individual pickstrokes. You learned it in chunks of six note units: one that starts on an upstroke, and one that starts on a downstroke. These are (probably?) separate motor programs in your mind, because that’s how you learned them. I’m not saying they are as different as throwing a ball as a pitcher and hitting a ball with a bat, but they are still different motor programs.
When you start a scale on an upstroke in the pattern you are playing here, you are asking your brain to string together four repetitions of the “upstroke chunk”. Let’s say, four repetitions of hitting a ball. When you start a scale on a downstroke, you’re stringing together four reps of the “downstroke chunk”, or four reps of throwing a pitch. It’s not a perfect analogy, but you get the point. They are two different activities, so it’s not surprising they might feel different.
Why are you better at batting than throwing? That’s the question.
The only specific mechanical guess I will make, which I’ve mentioned before, is that there appears to be a finger component to your technique. This was more obvious in an earlier clip where I believe you were playing 2nps type lines. It could be that differences in the type and amount of this finger movement may be related to these differences that you are feeling in the two motor programs you are comparing.
I liked the look of it in the pentatonic scale, it looks polished and consistent. Maybe take a look at that and see what you come up with. Also, when you sense that you are really good at a particular thing, I would definitely pursue more of it. Like, come up with other “inside motor chunk” type phrases that use this, and see how far you can take it.
In general, this is really excellent progress. You’ve surmounted most (all?) of the big obstacles and you’re getting to a point where all the polishing now happens at the level of small adjustments that you may not be able to see clearly, and that aren’t even always as awkward as you think they are going to be - as happened a few times in this very clip.