Disabling the Factory Security System

I have remote start / security systems installed on a 1998 Honda Accord SE and a 2003 Acura TL-S. The Honda's is a Clarion (self-installed), and the
Acura's is a Viper (second-source dealer installed). Both act the same when remote starting or opening the trunk: if the system is armed, the factory alarm goes off. The only way to avoid the problem is to unlock the vehicle before starting it or opening the trunk.
I've searched through the electrical shop manuals for both vbehicles, and can't find a way to use the "factory alarm disable" line from the remote start systems to disable the factory alarm system. Any idea how I can accomplish this, or where to go to find out? The guys who installed the Viper system said that Viper told them not to touch the factory system, lest dire results ensue. But I know that 'most anything is possible...
Thanks.
- John
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Some units supported, or had a module, that would unlock the vehicle (disarming the alarm), then starting it up, then relocking. See if DEI still carries this module.
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