if you are adding 5/8" plywood and then countertop thickness on top of what's there, won't that make up the difference? How high is the bottom edge of that drywall from the finished floor?

It's a lot better than the alternative! Don't panic - you'll find a good solution.

@palimpsest 37” is from floor to edge of drywall. 35.25” is from floor to top of cabinet. The 5/8” plywood will be added to top of cabinet. Countertop is 2cm so 3/4”.

Instead of trying to learn a whole construction and window installation trade, maybe just remark to the contractor that the window seems to be installed incorrectly, and it had better be fixed because it is upsetting to see it that way.

if it was mine i would of added the plywood under the cabinet. I have 2 cm quartz with ease edge slab. Your added plywood you will need a miter lip which also makes the quarts look thicker which may be the look you want so it really just depends if you like the thick counter look than the plywood on top will work if you want the 2cm slab thinner counter look then plywood under the cabinet bases and kickplate will cover.

But if you raise the counter height to meet the window, will that make the counters uncomfortable to work at?

She imagined the stone jogging in at every window opening to meet the sash of the window, versus ending at the face of the drywall. It is a cool look but not a hill I would die on here especially since the windows don't gain you much counter space. That said, if you really want this have the contractor cut out the subsill and drywall with a oscillating tool. It will involve cursing and the smell of smoke but then the stone could go up to the window as designed. You will likely need a small piece of trim (schluter? screen moulding?) to extend the window down to the counter.

"counter height" is vague & dependent on cabinet builder vs floor thickness etc.

Factory cabinets are typically built to net 36" w counter to be installed on top of finished floor vs local custom are taller and built to rest on subfloor

Typically windows are set to a "header height" unless otherwise noted (UON)

2 cm counters are always built up to 4 cm. 1.57" in other words. This is easily cured by the mitered edge of the countertop being very slightly higher, with a taller underlayment. It's a feature in lots of kitchens to have the thicker edge build.

Are you sure that you want the counter top to butt up to the window? Depending on where your sink is, you might want to have a "backsplash" so that water doesn't get into the wood of your window. You might also not like if someone leaves a window open or it leaks and water collects on your countertop.

My stone goes right to the windows (4), and I have had zero problems with water. My counters are extra deep on the sink side so it helps to keep window splashes to a minimum. I would do the counter height windows again in a heart beat...the light that hits the counters is wonderful, and the obstacle free transition brings the outside in.