because you have hands on access to the code. if either of those solutions do everything you need and you can afford it then by all means.
agoracart was designed for security first then user customization at all levels, limited only by ones creativity. there are some features that are lacking, such as quickbooks, but there are some, i am very sure, that have hacked the store to accomodate quickbooks. there have been customer recognition hacks integrated as well.
so it all boils down to how you, as the user, define your needs. start up expense, ability to customize html and some perl, time and more. I always tell people to go with the solution that fits your needs.
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