Gunnar Morling It is already working this way at the moment. Only collection of elements are stored as separate nodes.
I think the most natural and consistent way is to stored embeddable as separate nodes, There is already an issue for it: OGM-535

I'm prone to offer just the solution where we store them as separate nodes and only offer the option to store them as dot-separated if someone ask, Adding an option for this case seem to add complexity for not much value.