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.
My, admittedly weak, understanding is that the analogy is (much) more apt than not. Sure, the means by which that code is 'compiled' and 'executed' is much different than in the computers we've built, but, for one, DNA, genes, chromosomes, and all of the other various levels of organization of those units of information seem to be remarkably, amazingly stable, for many (most? almost all?) organisms, which seems to strongly imply that 'DNA is source code' is about as true as 'Earth is a sphere'. Sure, they're both only approximately true, but how approximately they're true (or not) is very important. Asimov explained this extremely well:
- [Asimov - The Relativity of Wrong](http://chem.tufts.edu/answersinscience/relativityofwrong.htm)
'Epigenetics' itself seems like it might not be a particular thing among different people:
- [The misunderstanding of epigenetics – Insitome](https://blog.insito.me/the-misunderstanding-of-epigenetics-a...)
What epigenetics is not is anything like Lamarckian inheritance, at least not at all to the same degree.
> Rearrangements, microchimerism, epigenetics, chromosome organization etc. are all things that exist and modulate information transfer beyond the standard four letters or the 'environment' (whatever people think it means) and we're still only scratching the surface.
Sure, but that doesn't mean that the central dogma of biology is entirely wrong, just that it's not always and everywhere true exactly. The current best understanding of epigenetics (quoted from my second link above) is that, whatever it is, it is such that:
> very little of [genetic] inheritance is perturbed by epigenetic effects