One thing to realize about consults (if these are truly consults you are filling out) is that per CMS guidelines, whoever is the author of the consult bills for the consult. That means, if the NP did the consult, the E&M code will be billed under the NP's provider number. As you know, the detail (or lack of detail) in the consult will determine the E&M code and the amount of money billed to the consult. With that said, consults are similar to H&P's in format with the exception of making sure there should be a "reason for consultation" (similar to chief complaint in the H&P) and "referring provider" (which identifies the primary provider who requested the consult).
What you leave blank in a checklist or pre-printed consult form just means the activity or the component of the examination was not done, either deferred or omitted by you, hence, you can not comment on any abnormal findings on your assessment and plan that you didn't find to be a concern to begin with.
Consults are done by specialty services (i.e., Cardiology, Pulmonary, Nephrology, Urology, and so on) at the request of the primary service (i.e., IM, Peds, and so on). Typically, these specialty consultants are only concerned with the reason why the service is consulted and will focus their recommendations on the body-system being addressed. For example, though Cardiology will be consulted for a refractory arrhythmia by IM, their consult will contain a head to toe exam but will be more detailed in terms of the CV portion of the physical exam and will maybe not mention "ugly looking toes". Their recommendations on the assessment and plan portion will focus on treatment of the refractory arrhythmia not the toe problem.
Where I work, we also have computerized charting. However, the consults come in different templates depending on what service is doing the consult. The template for the Critical Care consults we do are definitely detailed because we address all body systems in the ICU. Some services do not have a detailed template and only prompt the provider to answer problem-specific physical exam questions. That is OK because these other services do not recommend treatment that is outside their scope (i.e., Cards recommending a TURP - I know that is kinda extreme).
Update: read your subsequent posts, you are right in making sure toes are checked as part of a consult for diabetes. I would be very concerned that you are being asked to omit this important portion of the exam and management.