So I just used 5k Skystones in one go for this Shop just to see if the RNG on it is luck based or actually a rigged mechanic.

After my testing I can tell that if you don't use a lot of Skystones at once then you will feel like it's all about RNG but if you use "a lot" of Skystones you will notice a pattern, you either get lucky for a while and then super unlucky for a while or it will stay balanced.
In the end you will always end up with about 15-25% more then you would get if you just buy bookmarks, of course it's still worth it and you also get mystic medals which is huge but don't get fooled that this is about luck, it's calculated.

Or it is just a coincidence :)