What to ask, and why

Does flood cleanup include mud as well as water?
It should. Flood cleanup normally includes shoveling and extracting silt and debris before cleaning, sanitizing, and drying. Confirm it's in the scope.
Why is drywall removed above the water line?
Wet drywall pulls water higher than the stain shows, and the insulation behind it holds contamination. Cutting a strip above the mark opens the wall so it can be sanitized and dried.
Will my homeowners policy pay for this?
Outside floodwater is usually covered only by flood insurance. Report it to your agent and keep photos; ask the cleanup company to document the damage for whichever policy applies.
How fast will a cleanup company arrive after a storm?
Widespread storms create heavy demand across the metro. Call early, describe how much water and mud came in, and ask for a realistic arrival time.
Is it safe to turn the furnace back on?
Not until a qualified technician checks any appliance that was underwater.