Hi Rob,
mlti-core approach is different. You could have two cares lets say
marketing-core [Has its own schema.xml and data-config.xml]
magento-core [Has its own schema.xml and data-config.xml]

each core have their own schema.xml and data-config.xml
If you go by multi-core approach I guess you won't be able to achieve what
you described or what you needed. You can 
query across two cores but that is expensive and tedious.

The one you explained with having document type is just single core (Single
index) and you differentiate each 
document by their type

lets say document_type=marketing OR document_type=magento

I think you could go by having single-index (Single-core) with document_type
as differentiator.

Also note that if you have common fields between two databases, you don't
need to re-define those fields. 
You can make use of the same field for two databases.

Lets say you have field 'title' in marketing database and magento database.
You could have one 'title' field defined
in schema.xml, no need to define two title fields. Also carefully look at
each fields default values in schema.xml
Lets say you have some fields in marketing database and those fields does
not exists in magento db. When your done
with indexing, if the fields does not have values they will not show up in
the result. If you want it that way you 
don't need to define default="". If you still want to appear the field
regardless of data or no data you would have
to mention default=""
Ex:
<field name="year" type="int" indexed="true" stored="true" 
multiValued="false" <b>default=""*/>

To index two databases together, you can try with DataImportHandler.
In DataImportHandler you can query multiple data sources. Good thing about
DataImportHandler is that your datasource
could be data bases (MySQL, MS-SQL, etc), URLDataSource etc.

Hope that is helpful



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