I like your idea about the window, but I think you are reading too deep into it. A windowsill is what sits benath the window -- this does not necessarily mean indoors. Furthermore, people usually keep house plants on the inside of windows for sunlight, not flowers. Flowers are typically outside a window, planted in a horizontal (trough-like) pot. Imagine looking at a window from the outside with shudders, and then flowers below the window. That's not to say that people can't or don't have flowers inside near a window; I'm merely saying that you probably can't deduce that meaning from that particular lyric.
I like your idea about the window, but I think you are reading too deep into it. A windowsill is what sits benath the window -- this does not necessarily mean indoors. Furthermore, people usually keep house plants on the inside of windows for sunlight, not flowers. Flowers are typically outside a window, planted in a horizontal (trough-like) pot. Imagine looking at a window from the outside with shudders, and then flowers below the window. That's not to say that people can't or don't have flowers inside near a window; I'm merely saying that you probably can't deduce that meaning from that particular lyric.