I always comment on margins.. but do so like this:
"Intradermal melanocytic nevus, present at lateral edge and base of biopsy specimen"
This doesn't use the term "margin", and still tells them that the lesion hasn't been completely removed. I have never had a clinician take out a melanocytic nevus, which was called such without mention of dysplasia/atypia. I think it's good practice, at least with melanocytic lesions, to mention what the edges of the margin look like. So, if the site repigments, then at least you know that you didn't get around it.
For a paper regarding practices on margin reporting in melanocytic lesions, see
http://www.ncbi.nlm.nih.gov/pubmed/20846568
Practices vary greatly regarding reporting on biopsies. I think this is a regional effect, and that talking to your clinicians can help. I also tailor my reports to the dermatologist/clinician. As for benign non-melanocytic entities, I do not mention margins on hemangiomas, but do so on almost everything else.
J Am Acad Dermatol. 2010 Oct;63(4):661-7.
Histologic processing and reporting of cutaneous pigmented lesions: recommendations based on a survey of 94 dermatopathologists.
Kolman O, Hoang MP, Piris A, Mihm MC Jr, Duncan LM.