It is intentional that all logged output, including the command-line if that option is checked (or if logging of the default step property is enabled), is included in the LASTSTEP_OUTPUT macro.
What you could do is remove the first line of the output before processing.
Code:
Sub vbld_StepDone()
' remove first line of output, including CR/LF
out = Application.ExpandMacrosAndScript("%LASTSTEP_OUTPUT%")
out = Mid(out, InStr(out, vbCrLf)+2)
Builder.LogMessage "LASTSTEP_OUTPUT with first line removed:"
Builder.LogMessage out
End Sub