It's really annoying when the fields are shown after Gutenberg.
At the moment I have to use ACF instead of MB Custom Fields, to get the field groups shown on the side panel.
Regarding the meta boxes aside, it's already supported by MB Blocks. All you need to do is set the 'context' => 'side' for the block. Here is the docs for that:
I have a custom post type with custom fields. But when your in the Gutenberg editor, the custom fields ar shown after the Gutenberg editor, instead of the side panel.
In Meta Box Builder the option does not exist, when you select post instead of block.
This topic is about blocks, so I thought you're talking about it.
What you want is moving the meta boxes to the sidebar. That can be done with the same parameter 'context' => 'side' for meta boxes. See this docs.
Previously, Gutenberg moves all the meta boxes to the "after content" position, which is what you're seeing. It probably changed its behavior to accept side context. I've updated the Builder to reflect the change, so you can see the option within the Builder.