The Builder/pump will no longer consider flowing liquids as source blocks and so will no longer be a source of infinite lava
The Builder/pump will actually consume power now (cheaty cheaty)
By default the Builder will now quarry tile entities too! The old config option has been removed and a new one has been added so that you can disable this if really needed. However, tile entity harvesting should be safe and will go through the needed hoops to get all the drops. It is able to successfully pick up blocks that retain their contents and put the resulting item in the chest. Placing that item in the world later will correctly restore the tile entity. If a normal vanilla chest is harvested then the contents will drop on the ground though. Keep that in mind.
The builder in copy mode (with space card) and in build mode (with a normal shape card) will now correctly use the item in the input chest including all NBT data that is relevant for the resulting tile entity. Previously if you put (for example) a modular storage chest with a lot of items in it in the input chest (in item form) then it would consume that modular storage and place it empty in the world. Not any more.