A couple of things here.
First, the index thing was just a bug that was intrduced the same time as the tables when schemas were added as part of the criteria. So this was a very simple and easy fix and we checked to see if this would crop up anywhere else and so at this point things should be fine. A build is being created as we speak and will be posted in the next hour or so.
Now, a couple of things in regards to your expectations. The database import is intended to bring your structures, relationships, indexes, etc. in and then allow you to massage them and go from there. When you first post, you MAY actually see some tables be modifed that you are not expecting which is not an issue in many cases as extended properties are being applied, foreign keys updated, etc. In this case it was an issue since the indexes were missing.
Finally, the last thing that you should do is deploy to a production server the first time you are testing your meta-data. Obviously do a backup of your database, then copy it over, and test it on a NON-PRODUCTION database until you can massage and deploy as you are expecting.
Finally, the import tool in not intended to be a 100% catch-all. It gets you a long ways down the road and in many cases is 100% depending on the database. But like anything else...be sure to test on a non-production environment until you are getting the results that you are expecting.