So, MSI wrote and told me that it would be better if I did not use a 2.1 card.
You'll be fine.
The fact is there are no motherboards has a PCI-e 2.1 slot. Therefore, if a PCI-e 2.1 card does not work with a PCI-e 2.0 slot, then AMD will be loosing a lot of money since all Radeon HD 6xxx cards are PCI-e 2.1 cards.
Just try not to stick a PCI-e 2.1 card in a PCI-e 1.x slot. There maybe some compatibility issues unless the motherboard manufacturer released a BIOS update to fix the potential issue.