Can granite countertops be used as a desktop on a custom desk

The big difference as you mentioned is price. The seams with the pre-cut pieces should not be an issue (assuming the installers are good at what they do), the more noticeable factor will be the difference in colors and patterns.

If the entire counter is cut from a large slab, the colors and patterns will be consistent throughout the entire counter. If the counter is assembled with pre-cut pieces, you may notice differences in colors and patterns from one piece to another. The choice here, however, would come down to preference. Some people might prefer the look of one method over the other, so it's hard to say what you'll like better.

I would find out if they have a show room or can provide pictures (from previous jobs) of the different methods, then you can decide which you personally prefer (while keeping your budget in mind).

There are some distinct differences between Silestone and natural granite. Granite is cut from slabs and always has some color and patterning differences if you look closely. Also, if you can see the bottom of the slab at some point under the counter top, you will see the machine marks (groves) made during the cutting process. Silestone on the other hand is man made from granite chips and resins. A close look will not show the longer natural strands or runs and irregular shapes of solid colors as in natural solid cut stone. Silestone tends to be a bit more homogeneous in its overall color mix, especially seen on larger pieces.

Practically speaking, natural granite is a bit more porous that Silestone, and needs to be sealed occasionally to keep contaminates out of the tiny pores. Silestone is manufactured to be extremely smooth and non-porous and does not require sealing.