I can't find any specific mention of Syrian rue seeds being illegal in Portugal.
Here in the UK at least these plants are legal, as are the isolated alkaloids as far as I know...DMT on the other hand is a class A substance, but you can still obtain it in plant form without issue (although bulk buys of Mimosa root bark have been a source of negative attention). In London you can openly buy Syrian rue in Middle Eastern shops.
Syrian rue does have legitimate non drug uses such as a carpet dye, and I really can't imagine that a shipment of seeds would be picked up on...even if customs were to have a look at them I doubt they'd know what they were looking at. That list on the linked document was mainly targeting synthetic and research chemicals. On the plants/fungus section Syrian rue is not mentioned, so I don't think there will be a problem.
https://www.erowid.org/p...rue/syrian_rue_law.shtml