Yes, we also have the 'real' shallots here. They are sold as 'shallots' and are bought separately. We find them in amongst the other onions. The green onion/scallion/spring onion things are also sold as 'shallots' and come in bunches - we find them in amongst the salad veges.
Most people who talk about 'shallots' are referring to the things that are somewhere between a leek and a chive - the green onion/scallion/spring onion things. If we want to distinguish between these and the 'real' ones we say something like 'you know, the ones that look like onions'.
It sounds confusing, but in reality, not a lot of people use the 'ones that look like onions', so it isn't confusing at all - until I start talking about them to people on the other side of the world, in which case an explanation is necessary!