UPDATE
I wrote up my findings on this in a blog post:
http://www.ninjanye.co.uk/2011/06/getting-schema-information-from-edmx.html
http://jnye.co/Posts/3/getting-schema-information-from-an-edmx-file-with-poco
I came across this same problem myself.
First you need to retrieve the EntityContainer from the Storage Model Content (edmx:StorageModels) section of the edmx file
At the top of the tt template (after the MetadataLoader is instantiated and the inputFile is declared) add the following code to get the Storage Model Content EntityContainer
StoreItemCollection sic;
loader.TryCreateStoreItemCollection(inputFile, out sic);
EntityContainer sicEntityContainer = sic.GetItems<EntityContainer>().First();
Then from within the foreach (var entity in ItemCollection.GetItems...) loop you can get the current schema with the following
EntitySet eset = sicEntityContainer.GetEntitySetByName(code.Escape(entity), true);
string schemaName = eset.MetadataProperties["Schema"].Value.ToString();
Note: You may have to repeat the get schema code for ComplexType properties lower down in the tt template