I am not sure how microDNA ties with the diet and what are the implications, but as for microRNA, every organism starting from C. elegans and upper has their own microRNA. These are not epigenetic modifications, they are what is called post transcriptional modification where a gene is expressed and exists in messenger RNA form, then microRNAs degrade this gene to stop formation of protein. While it is true that plants have microRNAs, their effect is not studied deeply, humans have their own microRNAs which cause more important changes in terms of gene expression.
While microRNAs and post-transcriptional modification means a control on the mRNA of expressed gene, epigenetics prevent the expression of gene from the start, they are two different mechanisms. Yet, there could be lots of interactions between these two mechanism and how they relate to the diet, but plant microRNAs may not have roles as strong as we think.
Just my two cents, fwiw.