Here's the points at which this may not (or definitely does not) work:
1. the IBM DB2 dialect would need to support reflection of tables that are not in the default schema. Hopefully it does this already.
2. The autogenerate system in Alembic would need to include some way to configure it to also look in non-default schemas. The most straightforward way to do this might perhaps be that it runs through the given model metadata to collect all the schemas present so that it knows where to look. If you're interested in helping with this let me know.
3. the migration directives in op.* are in great need of more "schema" arguments, in most cases it's not supported. Help is also needed here, this is
https://bitbucket.org/zzzeek/alembic/issue/33/support-of-schemas-is-absent-for-most-of .
So the space for support is there, but not something I've needed myself yet, so patches/tests to get started would help this along...else I'll get to it eventually.