There's a big terminology gap here that we have to bridge.
1) Run In - this is what Lycoming does at the factory. So many minutes and such-and-such RPM, then so many more minutes at another RPM. That's RUN IN. Done for you at the factory or any half decent engine builder.
2) Break-In - this is what you are doing on the airplane (unless you have done the overhaul yourself). This is where you are running the engine hard at high power setting to seat the rings.
I can't think of any good reason other than the altitude consideration for a ground-based break-in. The engine will be getting great big gulps of cooling air when you do break-in in flight. Boring holes over the airport at 75%+ power setting isn't all that tough to do. You'll be getting to know your airplane, and your engine. Then if you're lucky you'll see that "aha" moment when the temperatures start to settle and you'd swear you can feel the engine running more smoothly.
Unless you have troubles getting the engine to produce full power, thanks to density altitude concerns, flying it seems the most reliable method of breaking in.
Oh, just thought of another reason you might want to break it in on the ground... If you're located at an airport where you can't be reasonably assured of short ground run times before takeoff and after landing then you might want to do the first few hours under a cooling hood.