The old version of the Smart Stop Start box didn't disable the remote start but if you used the remote start the Auto-Start-Stop would operational like you didn't have the box. The work around for that was to turn car off and start again from the driver's seat once you got in to disable the Start-Stop action. I didn't like that and returned mine when during trial period when I found the Range Tech device.
However, the lastest version of that Smart Stop Start device installs on the battery not the hood switch and remote start works as normal without enabling the Auto-Start-Stop. See it here.
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www.smartstopstart.com
The Range Tech device does same thing, plugs into OBD2 port. I used mine for over 3 years until I got Trifecta which disables Start Stop with programming.