No dilemma (yet). Simply remember to appraise apples to apples and to report comparable sales consistently to your subject. Then consider different client types may require you report these in a certain way; mortgage work for example (1004 form).
I see a two-story home with an exposed basement in your pic. I would separate the two levels above grade, from the one level below grade, on a sales grid/comparable analysis. Then I would state how much (a percentage or actual sf) of the lowest level was finished living space, and to what quality (quality the same as above grade? quality maybe less than above grade?).
The simple assignment would be where you have numerous sales of homes exactly like your subject, three levels total, two above, one below, with the lower level exposed. You may be finding however, the available sales are not exactly the same design (layout), yet still share a similar location, quality of build and general design, which would of course would render these relevant indicators of value, in my opinion (for instance you could have a two-story and a one-story, both similar in location, quality, living area and physical condition). I say in my opinion, because that is where it sometimes goes haywire and creates a dilemma. Other people will be reading, reviewing and using your report, and these people may not know what they are talking about, and might even decide they know better than the appraiser, despite the appraiser being the hands-on, trained, skilled and experienced expert. They might tell you only homes exactly like your subject are relevant and "acceptable" for consideration. That sort of dilemma, which is in my opinion much more of a dilemma than what you are wondering at this point, will be something you will learn to deal with on case by case basis. However, the most important thing, is to go back to my first sentence, which is to appraise apples to apples and report your data consistently. Good luck.
PS - Is there really a big difference between a Red Delicious and a Fuji? If so, is this the same type of difference between say, an apple and a banana? In houses, again in my opinion, most buyers value location, size (utility) and quality (design, component quality), and further if the home is no longer new, then physical condition as well. While conversely, buyers view one-story vs two-story as a personal preference or see no difference at all. You will find appraising is easy, while making your case to obtuse users is not as easy.
