You have definitely hit on one of the main limitations of lists (samplesets, assays, etc). That is flexibility of keys and indexes.

You very well may want to create a min-module to construct the tables you need. This may not be as hard as it seems at first glance. I'm not exactly positive what the absolute minimal module with schema is, but it may be as few as 3 files starting with

config/module.properties
schema/MySchema.xml
schema/dbscripts/postgresql/MySchema-0.00-1.00.sql

You can also toss in some predefined queries to get things started e.g.

queries/MySchema/UsefulQuery.sql

see https://www.labkey.org/wiki/home/Documentation/page.view?name=simpleModules