Excel templates of reports are controlled by the file
\secure\views\browser\report-excel.jsp. While you can't easily have different
report-excel.jsp for each report, you can easily edit the
report-excel.jsp file to behave differently for each report (or if you want, use a different include for each report).
The report-excel.jsp has full access to methods available in
com.atlassian.jira.web.action.browser.ConfigureReport. This means that you can figure out what report it is from the
getReport() methods, and make the page behave accordingly.