I'm not sure what exactly you're looking for, but yes, Craig Venter's team at JCVI and later Synthetic Genomics has been building synthetic organisms starting with Mycoplasma laboratorium in 2006. Most recently, an E. coli analog was built using DNA synthesis (https://www.nature.com/articles/s41586-019-1192-5).

To be clear, @aeorgnoieang's response is basically correct. The central dogma holds, the epigenetic program's role is well-characterized to be relevant to development/differentiation only under normal circumstances, epigenetic imprinting effects are weak, etc. As @aeorgnoieang correctly points out, the other things you cited (microchimerism, rearrangements, chromosomal organization/spatial effects) don't actually conflict with the "DNA as source code" metaphor in any way.

This is not to say that the popular understanding of these things is perfect - there are lots of misconceptions - but the way to fix that is by finding better ways to describe what we know and put it in context. A big issue is that as we learn more, media events around new discoveries make it hard to put the relative effects (of things like chimerism/mosaicism, polygenic risk factors, horizontal gene transfer, etc.) into context if you're not already an expert.