Doesn't matter... to the appraiser. The responsibility for requesting the correct appraisal service is the Client's. If they incorrectly tell you to appraise it as if the dwelling unit isn't there, then you can do that... for a fee. Of course, if you like the Client, you should spend some time chatting... educating them... that maybe what they are asking for isn't the best approach. Ultimately, it's their decision. Your decision is.... accept, decline, or withdraw.
USPAP is silent about forms. There is no prohibition against using the 1004 form for something like this... however, it's not a good idea. The built in statements and certifications on the 1004 would not really fit. In order to keep it correct, using the 1004 from would require a lot of extra commentary and it's highly likely that you'd miss something. Better off just using the GP form instead.
BTW, a fractional appraisal... that is an appraisal of a portion of a property... does not require the use of a hypothetical condition. It requires that the portions of the property being appraised be clearly identified and described. Sometimes though, it's simpler to just use an HC. If you are using an HC (or an EA) be sure to glance at SR 2-2(a)(xiii).