The difference between the excision codes (114xx/16xx) and the shave codes (113xx) is that the former is full-thickness (ie: cutting all the way down to the sub-cutaneous layer) while the latter is partial-thickness (cutting only into the epidermis and dermis). The former requires closure, while the latter does not. Both groups of codes are used regardless of whether or not a biopsy will be sent out.
The difference between these codes and the biopsy codes is that the biopsy codes are used when only part of the lesion is removed.
As for the penis biopsy code, we have always used 54100. I am guessing that the term "excision" in the title of that section of CPT is being used in a different sense from the way we use it in dermatology ("full-thickness, complete removal") and just means "cutting out something or a part of something" Just a guess...