Is the Miracle Cube package worth it?

It is more often... it is not a large amount. From my experience it's around a 10% chance to make secondary primary, which with 2 lines, really means 81% one primary, 18% two primary, 1% three primary. Within that 18% that's reasonable, you still need 2 good lines to hit - I just don't know if that's worth the extra money. Best case scenario is you get 40%+35% bossing instead of 40%+20%, but take 5 times as many cubes. You're much more likely to just get 1 good primary + 1 good secondary, and you only need supers for that.

The chance of extra primary lines with super cubes is not zero, either - it's just small. I would guess in the 2-5% range. All in all, I'd say you have something like a 1 in 10 chance that 2 good lines is primary+primary instead of primary+secondary by switching from super to enlightening.

By this he means that the chance to get lines that are not really significant to you (stuff like % chance to ignore static/% damage) is lower, not that the chance of primary on secondary/tertiary is higher (it is; it just isn't feasible enough for that to be the primary reason for their use over super cubes)