Hmmm, you're right.You're not disagreeing
In the embryo that scaffolding has to be setup by gradients and growth factors, etc While the cells contain the DNA to setup those gradients, I'm not sure you could say that tissue's truly self-organize (at least not in the way, you might think of a virus self organizing).
Its wonderfully demonstrated by growing tissue types outside the body. You can harvest a bunch of kidney cells and grow them in a dish, yet they don't self-assemble into a kidney. They require the interactions of friends of neighbors to do so (not to mention a host of other cells types, mostly connective in nature, to add any kind of tissue assembly).
I agree with the second part of your post, which is why I said in my first post on this topic;
Madcat8000: I don't know that I'd like to depend on a VERY distant relation to amphibians and render that code into an exon... then hope.