If you create a virtual layer for the legacy database in Teiid, and have all your applications using Teiid and this virtual layer to access, then you can insert logic into the "update" transformation for this table to create the auto-increment id, however you want it. Like select the last max id, then incrementing it and inserting it in that update transformation.
Currently there is no in-built support for this. However, if you like to see in future releases, please fill in a feature request in Teiid's JIRA. Yes, in Designer it is just metadata mentioning that it is auto-increment field.
If you are using Hibernate on top of Teiid, it has lots of built-in strategies to create the auto-increment field, so you could use that.
Hope this helps.