Try passing the settings file as a parameter to the scanner:
dotnet sonarscanner begin /k:"PROJECT_KEY" /s:"SETTINGS_FILE_ABSOLUTE_PATH"
When I was working on this a month or two ago I run into an issue, where the dotnet scanner was not be able to find the settings file using relative paths no matter where I’ve placed it, so do try to use the full, absolute path.
ps.: I’ve also noticed the scanner only read certain properties from the file, notably the ones that have a /d: parameter prefix when used as params, so eg. the project name, the project key and the project version did only work for me as command parameters (/n:, /k: and /v:) directly passed to the scanner on execution.