Application.cfc in virtual directory not being used

Originally posted here to address a different problem: Trouble getting web aliases to work - Communities - Ortus Solutions Community

I have a simple file layout for my app:

> project_root
   > tests
      > Application.cfc
      > runner.cfm
   > wwwroot
      > Application.cfc
      > index.cfm
   > server.json

and using CommandBox, I have a basic server.json file set up as:

{
  "web":{
    "aliases":{
      "/tests":"tests"
    },
    "bindings":{
      "HTTP":{
        "listen":"80"
      }
    },
    "webroot":"wwwroot"
  }
}

and I have configured a CF mapping for Lucee in .cfconfig.json:

{
  "CFMappings":{
    "/tests":{
      "INSPECTTEMPLATE":"",
      "PHYSICAL":"system/path/to/project_root/tests",
      "PRIMARY":"physical",
      "READONLY":"false",
      "TOPLEVEL":"false"
    }
  }
}

When I went to http://localhost/tests/runner.cfm, I noticed that the template in that virtual mapped directory (tests) was not using the Application.cfc in that directory. Instead, the Application.cfc file of the webroot (wwwroot) was being used. I was expecting the Application.cfc of the current directory to take precedence, so I’m a bit confused why this is. Is it related to Jira luceeserver LDEV-694?

Using with CommandBox CLI 6.1.0+813.

OS: Windows 10
Java Version: 11
Tomcat Version: 9
Lucee Version: 6.1.1.118 and 5.4.6.9

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