You have a good question there and the answer is you need to compromise something when you road kill the body.

I like to build the plan form exactly as the 3-view shows with the LE & TE of wing and tail plane extended to where they meet in the middle.  Thus, the wingspan and tail span are correct.

The wing area that was trapped inside that body is liberated.  In virtually all cases, the model can use all the wing area it can legally get.

A bigger problem is the landing gear of a prototype that had a "wishbone" type of gear mounted in the fuselage.   It ends up being too "narrow-track" for it's own good.

I have submitted a rules change proposal to answer this recurring question.

See Rules Change Proposal CLS 11-9.

Clancy

It seems to me that this proposal, which makes mandatory Paul Smith's approach to profile wing problems, has not been completely thought through.  If you accept that a scale model, even a profile model, should aim to recreate the "feel" of the prototype then a rule like this would damn many prototypes to be either unusable for a profile model or doomed to ridiculous distortions.

A few examples:  The Spitfire or Thunderbolt wing would lose its elegance with a constant-chord addition which would look worse and worse as the scale grew larger.  On a Hurricane or Avenger the straightish center section would assume a wholly different relationship to the strongly-tapered outer wing.  A Stuka or Corsair would be a complete disaster with the inner gull section forced into either a grossly different dihedral angle or an attach-point way higher on the fuselage.

This proposal is just way too rigid.  If, as the proposal states (and it's a good point), that some guidance for the judging considerations and a contestant's design decisions should be in the rules, how about: 

"Profile scale judging recognizes that severely narrowing the fuselage will affect the wing in some way.  Scoring will be based on the modeler's success in retaining the character or "feel" of the plan view of the prototype. To accomplish this the modeler may choose to shorten or lengthen the wing in whole or in parts and/or unnoticeably (generally 5% or less) increase or decrease the scale of the wing in relation to the fuselage.  Since the models are not measured changes in scale span size are not important, but overall appearance is."

Guys, it's "artistic" decision, but we make lots of those with every model.  Color shades, paint gloss and adding or omitting details are similar. Lets just state the goal and leave it to the modeler.