Yes, you could use a cartesian join to the issues table, then filter the portal to that table to display only where: Company::Identifier = Issues::Ref1 OR Company::Identifier = Issues::Ref2.
Might be easier though to setup a proper many-to-many relationship though, as using a cartesian join can lead to performance issues down the road for displaying portal records.
In addition to Mike's point (which I agree with,)... "Portal Filtering" is ignored by functions like... Sum, Last, List, Average, Count, etc... and by script steps like GoToRelatedRecord, thus only the actual relationship is evaluated. That being said, there are many times when Portal Filtering is handy, like a popup search/selector referencing a low volume table. If the table being referenced holds a high volume of records, it is best to use the relationship to filter down the list, then perhaps use a Portal Filter to refine that set, (keeping in mind the Function issue.)