Seat62K
I've managed to check in online with easy, despite having declared a suitcase when booking, so I assume the systems don't cross reference on bags.
In fact, I used your argument to the check in agent when she had a strop.
'Surely, if this should not be done, your integrated systems would not allow it?'
I have to admit that I did not see the 'hand luggage only' caveats.
Alexpilot, the outcome was I got checked in after some muttering, so I wouldn't worry.