Reproduction steps:
1. Create a new project
2. Import contents of "ASMFILES.zip" into the assets folder of the project
3. In Editor, select Assets/IndependantScripts/IndieDef.asmdef
4. Notice that it has "No Engine References" enabled in the Inspector
5. Open the root of the project and open "IndieDef.csproj" using Rider Editor (read Notes 1, 3 below)
6. In the Solutions tab go to IndieDef -> Dependencies -> Assemblies
7. Inspect the References

Expected result: There are no references to Unity (exceptions would be platform related Assemblies such as UnityEditor.iOS.Extensions.Xcode and UnityEditor.iOS.Extensions.Common)
Actual result: There are references to UnityEditor, UnityEngine

Not reproducible with Windows

Reproducible with: 2019.4.18f1, 2020.2.0a8
Not reproducible with: 2020.2.0a9 (Fix version), 2020.2.2f1, 2021.2.0a2
Could not test with 2018.4.31f1 (because .asmdef file does not have an option to not include engine references)

Notes:
1. The references can be seen in Visual Studio and other IDEs as well but sometimes Visual Studio does not show references
2. The issue should not reproduce because IndieDef.asmdef (located in Assets/IndependantScripts/IndieDef.asmdef) import settings has "No Engine References" enabled
3. Sometimes the csproj files do not appear in the root after import, to generate them open IndieDef trough editor and close it