Hi Mikko,
Nice thought! Many similarities. But remember the Batavia was built 1625 as a (Dutch) East Indiaman, whilst HMS London (1656) was an already further evolved warship, three decades later. The first glaring difference is that the sheer of the later ship is much less, and the gun ports don't follow the sheer anymore.
I haven't studied the British warship kits of the 17th century, but from the Dutch ships available the Eendracht would be a better comparison. The Revell kit of 'Wappen von Hamburg', which has also appeared as the Lindberg 'Captain Kidd pirate ship' (surprised?) is a much better representation in 1:150 (surprised again? The scale with these old Revell kits is often far from the figure given on the box

).
The reason behind this: the Wapen von Hamburg (the correct spelling then was with a single p, and her sister ship Leopoldus Primus) was built by a Dutch shipbuilder master, on the pattern of the then famous Dutch 'two-decker'. As no plans of the Wapen have survived, the model must have been created after the Dutch plans for these two-deckers, the Revell/Lindberg kit being the result.
As a model kit it is truly awful, but if you plan to build such a ship it could be a good basis. I'm already working some time to convert the kit into the Aemilia of 1632, I made a completely new transom plus adjoining galleries, but for the rest the kit could largely remain the same.