We do alter the genetic material in 'traditional' artificial selection and given the current genetic sequencing methods, we could definitely demonstrate the pathway we'd have taken if we were doing it 'slowly'. But if a crop takes ~6m to become mature enough to reproduce, we'd easily take decades for a simple mutation. Doing it in a lab allows us to skip some steps but you get the same end result.
I don't agree with the patents but AFAIK none of our food is patented nor could it be. I think gene patenting has been completely struck down recently. Yes, there has been research in a terminator gene and it made big headlines a decade ago but further research proved that nature has a way of overcoming these artificial limitations. There is currently no crop outside of a lab that cannot reproduce itself (besides dessert banana's, but that limitation has been around for about a hundred years).