How to proceed in a patient whose mole's biopsy report has been diagnosed as mildly atypical, depends on the philosophy of the dermatologist.
Atypia can be either architectural or cellular. Architectural disorder means that there are some irregular features in the general shape and configuration of the mole. Cellular atypia means that some of the cells may have a nucleus that is too large for the size of the cell, or the nucleoli look off-color. Cellular atypia is more serious than architectural disorder.
Many dermatologists will consult with the pathologist. If the pathologist is confident that the mole will not behave badly, he/she may advise us to leave the mole alone, that no further surgery is necessary. These dermatologists will request that the patient return if there is a sign of pigment recurring. Some dermatologist are not comfortable with this approach, and will excise the entire mole.
I prefer an excision of an atypical mole rather than a punch biopsy. I feel there is a better cosmetic result, especially on the larger excisions. I disagree with the PA that the punch biopsy goes deeper; the depth of the excision and the depth of the punch biopsy would be the same. However, if the punch biopsy is well around the scar of the mole, and the pathology as returned that there are no residual nevus cells, then, otherwise it would not matter.
One other thing. I find nothing wrong with a PA examining you first. However, I hope that a dermatologist followed up this examination. There are too many practices where a PA is acting as a dermatologist...not with the goal of improving medical care, but for the economic benefit of the dermatologist. If the PA examined you and THEN the dermatologist, that is fine, since four eyes can be better than two.
In regards to the shave, I would assume that your pigmented lesions drew little suspicion of a melanoma. In such cases a shave biopsy can be safely performed. The vast majority of melanomas begin high up in the skin. However, if a melanoma is suspected, either a saucerization technique ( essentially a deep shave) or a total excision should be done, not a superficial shave biospy. Dr. June Robinson showed in a paper in 2008, that a saucerization technique was as effective as an excision. In some cases, with a large atypical pigmented lesion such as a lentigo maligna ( Hutchinson's freckle), this method may even be preferred.