You may possibly be able to exclude this second building from the certifcation scope, but you'll want to look carefully at the MPR Supplemental Guidance document for MPR # 3, Site Boundary on pages 12 -19 of
http://www.usgbc.org/ShowFile.aspx?DocumentID=6473.

In particular, see if the second building would be in your judgement "associated with or supports the normal building operations" of the first project.

It may be too big to meet the exceptions for small buildings within the project boundary described on page 19, but there may be a reasonable site boundary for the first building that would not include the paint touch-up building and it's supporting site area that wouldn't be seen as "gerrymandering."