Look at it this way.
If Rowlet was pure Grass right now, it would be kinda weird, right? It's an owl. It can obviously fly. They didn't really have a choice but to give it the Flying sub-type. Upon evolution however, I could see it losing the ability to fly through significant physical change as you mentioned. I'm not saying it's definitely going to happen, but it's possible.
Yes, it would be really weird if it were pure Grass, which is why it wouldn't guarantee a Grass/Flying future. I really don't see it changing, and sure, anything's possible, but I just find the likelihood of that change to be fairly low.