1) While the tooling support like the JPA Details view and validation may not work (you will have to turn metadata analysis off on the MyEclipse > Java Persistence property page), it should still be possible for you to reverse engineer.
From the DB Browser view, select the tables you wish to RE and choose “JPA Reverse engineering” from the context menu. The tool will not however allow you to reverse engineer from tables in multiple schema at the same time, however, you can do this in two separate passes. Cross schema relationships, if any, will not be picked up by the tool.
Could you tell us a little more about your environment?
a) What database are you using? Are you using a database like MS SQL Server / Sybase where you have multiple schemas in a catalog?
b) Do you have relationships between tables in different schemas?
2) Unfortunately it is too late to fix this for 7.0, but we will take care of it in the first release following that.
Sorry for the inconvenience caused.