I set most of SIS (System Information Stream), Add/Remove Programs, Product Property information with Options.ini, and my .ism's reflect none of these entries.
With AS5.5 you could try to create a default ism with all your ARP, Summary Info Stream, Product Info information and set that as your template in the "Customized template" option, under the repackages output tab within isrepackager.
This appears to be an issue with the conversion to ism/msi - certain properties are not overridden by Options.ini settings. We will look into this for the next release.
