Making levels in Blender feels a little backwards
Why? That's a perfectly valid way to do it, and it's generally the approach "power users" take. The feature set in an engine's level editor can't really compete with dedicated tools. For example, in Blender you can make use of geometry nodes for creating procedural content. Big (or at least funded) studios typically use Houdini.
For Godot, read through this section of the docs to leaen how to import collisions