Usually we use the same system that Jeff Yates mentioned with minimal (often single-line) stub patterns, including a common pattern.
You can also use Oleg Sych T4Toolbox to output the project to any directory that you like.
However, the standard IVsSingleFileGenerator on which the custom T4 tool is built does not have any dials to access output location management, and this is the case for linked files as you describe.
Garethj
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