Unfortunately, the ability to set the binding's SendTimeout on a per request basis is not available.
I'm assuming the values on EntityQuery that you were referring to is the CommandTimeout. You can't use this timeout for RPC as this is a different timeout for a different purpose.
There are different timeouts in the .NET world.
1. Database timeout - Can be set by using EntityQuery.CommandTimeout
2. Transaction timeout - Can be set by using the TransactionSettings which in turn passed into the QueryStrategy
3. WCF communication timeouts - These are the sendTimeout, receiveTimeout, etc settings in the .config file.
4. and finally IIS timeouts