The solution will be to always have a column alias EXCEPT for subQueries.

That is if you use the in subQuery expression on the where clause Ebean will not add column alias for the subQuery columns.

Query subQuery = Ebean.createQuery(Product.class)
.select("id").where().idEq(4).query();

List list = Ebean.find(MinCustomer.class)
.where().in("id", subQuery).findList();

select c.id c0, c.name c1, c.notes c2
from o_customer c
where (c.id) in (select p.id from o_product p where p.id = ? )

Ebean will always include a column alias except for sub queries.