Hello,
To prototype whole of your level, you can place primitives to level and modify them on level editor if necessary. Modifying static mesh geometry from static mesh editor is just an option. As you do with BSP, you can place primitive shapes, move their faces and edges, insert edge loops, and extract faces, directly on the level editor.
As @KAIRA_Deepware described above, I feel Mesh Modeling Tool is upper-compatible with BSP tool. I can do everything I did with BSP and enjoy more advanced feature on Mesh Modeling Mode too, except for subtract operation.
The Mesh Modeling Tool’s “boolean” operation is not compatible with subtract operation in BSP (you can’t move subtraction geometry. Boolean operation change your geometry permanently.) On the other hand, converting graybox geometry having holes to Blocking Volume is more precise than old one. For me, this advantage overshadows the disadvantage.
I hope my reply helps.
Thanks!