I contacted BL support and they replied:
Thank you for your email. For the first time with the release of a Limited edition book it was made available on the Games Workshop web store as well as the Black Library web store with the stock split between the two web store. Unfortunately the stock of the Limited edition Magos book sold out very quickly on the Black Library web store and then sold out a day later on Games Workshop.
Also wanted to know if they plan to split stocks for the future as well and got reply:
As far as I know this was done as part of our celebrations only, we have not received any notification that this will happen with future releases of Limited edition books.
Good that it was just one time action. I am now postponing some purchases like Primarchs LE's and this was quite unexpected. Still, from now on I will have to watch closely each release. It is a little bit problem as date and time is not always the same as for weekly releases on GW site.