Hi there,
The naming convention for new registry table entries can't be changed when working with the UI.
One solution would be to use the automation interface to change the names in the registry table before exporting the components into the new ism.
If you don't fancy coding, instead of exporting whole components, try exporting the registry ones into reg files hkml.reg, hkcu.reg, hkcr.reg and import them in your new msi.
Tip for msi from multiple isms: When converting your repackager output, use the first ism as a template for the second ism, the second ism as a template for the third and so on. just change the common component names in the previous ism first (i.e. RegistryData_Machine to RegistryData_Machine_App1)
Good luck,
Marco