how can you index a 9 speed 11-46 tooth cassette if the gears arent equally apart

Once the cassette is mounted and the lockring is tight, the cogs should be equally spaced. To my knowledge, Shimano and SRAM cassettes have all had equal spacing between cogs.

A side note: Campagnolo is the sole exception to this. Their loose spacers are not equally thick. I think their rationale is something about improved shifting. In practice, for their 11s cassettes, you can't visually tell that the cog-cog spacing is uneven once installed anyway. Anyway, their shifters have a ratchet which controls how much cable is pulled with each shift. That's how their system indexes the gears. If you mounted a 10s or 9s Campagnolo cassette on a Shimano system of the same number of speeds, you might be able to adjust the gears to shift acceptably, although it would be a lot more prone to coming out of adjustment. At 11s and up, the differences in cog-cog spacing are so small that the cassettes are actually interchangeable.

It sounds like you're talking about the tooth difference, and not the horizontal spacing between cogs. Most cassettes are "uneven" in this sense. It does not affect indexed shifting, so long as the derailer can accommodate the max number of links difference and can "reach" as high as the largest cog.