This is a tough one to answer definitively. The FCRA/FACT Act does not define an application, or at least I have not found where it has.
g) Disclosure of credit scores by certain mortgage lenders
(1) In general
Any person who makes or arranges loans and who uses a consumer credit score, as defined in subsection (f) of this section, in connection with an application initiated or sought by a consumer for a closed end loan or the establishment of an open end loan . . .
Would a pre-qualification request/application be an application for a closed end loan - IMO yes. It just wouldn't be one for notification requirements under Reg. B unless it resulted in a denial. Also, are you using the credit score in relation to the pre-qualification "application"?
To make a long answer longer, - IMO you should provide the notice. However I will admit this opinion is based on my personal intrepretation.
The opinions expressed are mine and they are not to be taken as legal advice.