While it's true that countless genetic manipulations are possible with E. coli, I wouldn't use it as a basis for synthetic meat, mainly because it's a single-celled organism. You would need to put an unreasonable amount of effort into teaching E. coli how to build multicellular structures. I don't think it has ever been done before and I presume it would take decades if anyone even wants to pursue that path. It's much more practical to use cells that already know how to form multicellular structures. All you have to do is convince them to grow outside of an organism. And you could get the inital cells from biopsies that don't do much harm to the animals, so I don't think there would be any ethical problems.