The reason why relational processes in polar interrogative clauses such as Are you crazy? do not exhaust the thematic potential of the clause is that the experiential weight of such clauses is in the participants, not the process. That is why Theme extends beyond the Finite/Predicator to include the Subject as well.
Here are the relevant quotes from IFG3.
How To Identify Theme
Halliday & Matthiessen (2004: 85):
… the Theme of a clause extends from the beginning up to, and including, the first element that has an experiential function — that is either participant, circumstance or process. Everything after that constitutes the Rheme.
Theme In Polar Interrogative Clauses
Halliday & Matthiessen (2004: 75, 76):
In a yes/no interrogative, which is a question about polarity, the element that functions as Theme is the element that embodies the expression of polarity, namely the Finite verbal operator. … but, since that is not an element in the experiential structure of the clause, the Theme extends over the following Subject as well.
The Experiential Weight Of Relational Processes
Halliday & Matthiessen (2004: 213-4):
… the experiential ‘weight’ is construed in the two participants, and the process is merely a highly generalised link between these two participants … Thus the verbs that occur most frequently as the Process of a ‘relational’ clause are be and have; and they are typically both unaccented and phonologically reduced … This weak phonological presence of the Process represents iconically its highly generalised grammatical nature. The limiting case of weak presence is absence; and the Process is in fact structurally absent in certain ‘non-finite’ ‘relational’ clauses in English … and in many languages there is no structurally present Process in the ‘unmarked’ type of ‘relational’ clause … Here the ‘relational’ clause is simply a configuration of ‘Be-er1’ + ‘Be-er2’.