When we run the extractors for invoices the GI/IR is the account that we are seeing in the data. Is this what we should expect?
yes that is what is expected. And your comment on of being little value is true as well. This discussion came up in one of our implementations - cant remember from top my head what the work around was. But this is what I think (may be this is the solution I put in place - or if this was already addressed in 3.0) - in the datasource extraction kit you can change the logic accordingly. If a invoice is referenced to PO, then get the GL from AK/IK tables (invoice level) instead of BSEG (a/c doc). Simple fix. And this is not addressed in the BI transformations.
And why are implementing 2.1 when its been more than a year 3.0 is out?