1. Don't know what gameplay you watched, but I haven't seen that with the ones I watched, and even then, lore > cutscenes >>>>>>>>>> gameplay.
The first time they meet, she's in Purgatorio.
2. She doesn't use witch time to draw on his face.
https://youtu.be/9LoKV8HK5kc?t=26s
She draws on his face from Purgatorio (he says "What the?") and that purple flash is her coming back to the real world, evidenced by the fact that he could now see her.
3. Her fight with Sapientia uses Purgatorio once again, not witch time. Not really impossible either.
She clearly crosses over into Purgatorio and Luka zips up. As he is doing so, he looks down and surprise surprise, no Bayonetta, and instant proof witch time wasn't used. As she surfs up to the chopper, she comes back into the real world.
Further proof witch time wasn't used:
-The entire boss fight gameplay wasn't in witch time
-The raging storm and sea are moving at full speed
4. I already made clear the fact that Bayonetta uses her abilities within each dimension with the Enzo scene.
First you see her activate witch time (which has no portal indicator), then she creates the portal for Purgatorio to jump through. 19:22 - 19:31
https://youtu.be/9QYQ3Dk3_Cg?t=19m20s
She leaves Purgatorio here
https://youtu.be/9QYQ3Dk3_Cg?t=21m58s
And you can see the difference, because the first purple circle leaves Purgatorio, the second one cancels witch time.
Further proof: -She activates witch time in the real world, goes to Purgatorio where the motion of every living thing an object is unhindered
-She encounters Jeanne, then witch time is activated applying its time slowing effects, since the angels are now moving in slow motion