Hi @abalter, I think you are hitting a key point. It is difficult to reproduce fold change mainly because it isn't possible.
It's not possible to infer absolute differences from relative data.
See our paper that just came out here: Establishing microbial composition measurement standards with reference frames | Nature Communications
These concepts apply to DESeq2, since DESeq2 assumes that the median for each sample is constant. This may not be a good choice of reference, and alternatives are discussed.