if they roll up to the same subsidiary and that subsidiary has a different currency, then you should be able to specify different rates. If it's the same currency, then you can't.
Note if these differences in rates are arising from ancient history, it might be possible to just put the historical entries in different periods before you went live in Netsuite and force the rate that way.
If that doesn't work, you need an intermediary parent with a different currency for one of the subs - Netsuite can help with setting this up - or you can post elimination entries to achieve the consolidated fx outcome you need, or you can get a third party consolidation tool