90 thousandths is ABSOLUTELY LUDICROUS. Even if you measure it up/down, it should be nearly impossible to have that much slop and be safe. Basically balljoints are constructed with a sintered iron cup and a steel ball with a tapered shaft extending. There is a rubber bushing (or spring in some cases) that pushes the slack out of the balljoint. If it is healthy, there should be NO SLOP. Unless you REALLY tweak on it.
That 90 thousandths thing... I'm gonna do the math on how much wheel wobble that would equal.
The balljoints are about 8" apart eyeballing, so that means .090" would be doubled if it's the bottom one .180" with the slop, and still .090" if it's the top give or take. I almost wonder how they are measuring it. If that's the slop at the balljoint, I think that is just WRONG of them to allow. I just can't imagine almost 1/4" of slop at the edge of the wheel being ok.
If your allignment guy says it's funky I would be inclined to agree.