Certainly it will be. The top-of-the-line Model 3 will be more expensive than the bottom of the line Model S. Compare any given BMW, Mercedes Benz or Audi line from top to bottom and you'll see it clearly. Bottom US BMW 3 is $34,145 and loaded top is ~$99,000. Current Model S ranges from $70,000 to $144,500.
Model 3 top-of-the line will almost certainly be around $100,000. That is my budget for the one I'll order and I expect no change from the budget. I definitely would not want a stripper with no autopilot, RWD, and so on. Some people want the basic one. That is why every car builder builds a wide range in the same vehicle line.