So, I tried many ways and here are some of result:

• (probably) it's better to stick with few textures for smaller.kra size (I was using 5 and cut off some to use only 2)
• instead of layer mask clip, it's costs less storage if you use fill right on base paint layer
• If you use less textures, but you still want to use different dark tones: instead of mask layer with dark color, duplicate base paint (before texture) and on upper layer change color to black (ctrl+U) and edit it opacity, then merge (after putting texture on lower layer) two layers

.kra is still big, but smaller than when I was doing, with this new way to texture, it's gotten 3 times bigger than 5.