Why do many resistor kits deviate from E6/E12?
It depends why the kit has been put together.

If you buy a lab kit of E24 values, then you get a book with 50 of each value from 10 ohms to 1 Mohm, in the full E24. 

If the kit has been put together to support a set of tutorial designs (my first kit was part of the 'Phillips EE20 Electronic Engineer Kit' which had germanium transistors in it), then there's no need for the full range.

Think about what resistors are used for. It's typically to set up a ratio, at some reasonable impedance level. The impedance level can be fairly coarse. As a designer, I rarely think tighter than 'does it have to be at the 1k, or the 10k, or the 100k level?' However, I often want to nail the ratios to a few percent, and be able to set ratios over a wide range.

Resistor ranges are constant ratio (or very nearly so). To take E24, I can can set up a 2:1 ratio with 1k/2k, 1.2k/2.4k, 1.5k/3k, 1.8k/3.6k, 7.5k/15k, and maybe a few others if I think for longer (like 1.1/2.2). I don't need all those pairs in my kit, just one pair in each decade will do for 2:1 ratios. And a few more for a few others. 

Because of the economies of scale, it's far cheaper to provide a tutorial kit with 20 each of a dozen different values, than 5 each of 4 dozen values. It needs less organisation, and a smaller box, as well. Whether those values are from the E6 or E24 series makes very little difference to the price, E24 is used so widely in industry. What does make a difference is tolerance, but I'd probably want to use 1% throughout for a tutorial kit anyway.

As an aside, once the book has been in use in the design lab for a month, all the 1k and 10k resistors have gone! It's possible (just sayin') that designs end up with 1.2k resistors in them because all the 1k resistors had gone when the designer came to prototype it!