I've figured out a solution using VS Code workspace.

You can create a .code-workspace file that references both project folders:

sample.code-workspace

{
  "folders": [
    {
      "path": "A"
    },
    {
      "path": "B"
    }
  ]
}

Opening this workspace file will then display both projects (A and B) side-by-side in the "Java Projects" view, and the Spring Boot Tools extensions is working.