I'm glad you asked. There are two main differences:
1. X3 is 9" taller (66" vs. 57")
2. X3 has the SUV/CUV look (aka two-box shape)
Ride height/seating position is important, but the look is what really matters. A look that conveys strength (aka safety) and rugged adventurism is paramount. All the other things people claim motivate SUV/CUV purchases - passenger seating, cargo space, handling, ease of ingress/egress, price, fuel economy and safety - are just rationalizations. Otherwise they'd buy minivans, which win by a landslide on all counts while offering the same ride height/seating position advantage.
So, let's estimate Model Y's market impact using my wildly popular Market Impact Score metric. SUV wannabes can score a maximum of 10 points on ride height and 20 points on rugged SUV look.
BMW X3 - 25 points. 10 for ride height + 15 for look (good 2-box shape, but more streamlined than rugged)
BMW 3 Series Hatchback - 2 points. Only 2 inches taller and looks almost identical to the base sedan
Tesla Model Y- 5 points. It's 5 inches taller, but also looks almost identical to the base sedan
So there you have it, scientific proof that Model Y's market impact will be a bit more than BMW's Series 3 Hatchback but much, much less than the X3