Nominally, high-quality dark chocolate is made of just two things, cocoa beans and sugar. In reality, nobody just chucks beans and sugar into a machine together. The cocoa beans get processed to different intermediate cocoa-derived products, and these get mixed with sugar to make a chocolate bar.
The cocoa-derived products can be very different. There is a range from cocoa butter (100% fat) to low-fat cocoa powder (about 5% fat, the rest is basically all carbohydrates), with other products with a fat content between these two extremes. The difference in fat comes from simple mechanical separation - once the cocoa butter has been "churned" from the cocoa liquor, what is left can be milled into cocoa powder.
The 90% number printed on the package means the total amount of cocoa-bean derived products. But their combination does not have to resemble the nutrient composition of a raw cocoa bean, it can be chosen by the producer any way they wish. So, apparently, Lindt Excellence uses a higher percentage of cocoa butter (or other fat-rich cocoa products) than Amedei Toscano Black.
If you are wondering about the sugar content being different, note that the ingredient "sugar" (the 10% added to the 90% cocoa) is not the same thing that gets counted in the nutrition label, where any sugars (including those already present in the cocoa bean) are included in the calculation. See this recent question for a longer explanation.