Looked at your photos, and the Magnaglide azimuth adjustment bracket (is also the mount for the anti-skate cantilever tether is definitely not perpendicular to the vertical bearing well shaft in the first one. The second one, while still showing the misaligned bracket, is actually normal; the unipivot assembly is unbalanced when the arm wand and cartridge are removed, so will be grossly canted toward the counterweight.
The video clearly shows the motion is whacky. While not removing the protective bearing cap would definitely cause funky motion, that doesn't account for the azimuth bracket being out of square. I can't see all of my bracket area clearly because my table is in a recessed wall unit, but I did check the manual, and I didn't see where that bracket has any user adjustment. The bracket should rotate smoothly around the bearing well shaft through an arc of maybe 30 to 40 degrees and have a strong magnetic attraction to the unipivot assembly when next to it. I seem to recall that the Magneglide assembly was very elaborately packaged when I received it, so it's probably sensitive to shipping damage.
I'd guess the bracket is missing a part on the interior circumference around the bearing well shaft. You could give Bob Graham a call to see what he says, but he will likely refer you back to your dealer in your case. I ran into a problem with balancing mine with an ultra-low mass cartridge and contacted him. He promised to get back to me and never did. Through empirical testing, it turns out the Supreme can't balance and set proper VTF with carts of less than about 7 grams, even though the manual says it can handle carts as light as 5 grams.
In spite of all that, once I got it working, I can honestly say the Phantom Supreme is one of the best tonearms made, period. It tracks beautifully and enables my (heavier) cart to reveal details I never heard before. Patience is a difficult virtue, but it will be rewarded when dealing with vinyl.
Good luck and (when you get it sorted out) happy listening!
