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"Do not save encrypted files to disk" IE setting - How far does this go?

Hello all,

 We are getting ready to implement a new software on our network and the client which is an excel add on has a diagnistic check.  This same client is also used for web access to this software but we do not intend on using that web piece, rather just the piece that is built into excel.  This diagnostic checking reports an error on all of our computers becasue we do not have the "Do not savge encrypted files to disk" checked off in IE settings.  I am reluctant to make this change to all of our computer through GPO as I am not completely aware of the negative implications this could have with other web apps.  
My question is, this setting in IE, does it effect a client using http protocol OUTSIDE of IE?  If this isn't relative to the NON WEB access of this application we will be utilizing, then perhaps it is a mute point and we can just forego the diagnostic error.
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This is what I thought, I wanted to be sure though. Thank you.