As far as I know they are still treated as separate parts of the LEGO Group.
Nope Lego Family purchased Merlin so all same people ...
The Discovery Centres are owned and run by Merlin Entertainment, so are separate entities from the official LEGO shop. That's why they have their own exclusive sets. I discovered this when trying to use a LEGO Shop gift card at a Discovery Centre and was told I couldn't use it as they were a different company.
I believe its been set up to sell stock that would otherwise had been sat collecting dust, though I don't know why they didn't just sell the exclusives on the official LEGO Shop.
Should be working now