An atypical nevus is a melanocytic lesion that lacks the specific features of a BCC, such as a pearly, rolled border or surface telangiectasias.
A pigmented intradermal nevus is a benign, dome-shaped mole, lacking the malignant features (ulceration, pearly border) of a BCC.
A junctional nevus is a completely flat, benign macule, whereas a pigmented BCC is a tumor that, even if flat initially, will have other subtle features of malignancy.
This is the most important differential. Melanoma is often more variegated in color and more irregular, while a pigmented BCC often retains some classic BCC features like a pearly border or arborizing vessels on dermoscopy.
A pigmented SK is distinguished by its waxy, "stuck-on" appearance and often has horn cysts visible on dermoscopy, which are not features of a BCC.