Your observations are correct. GoAnywhere is designed to use the resource credentials to choose paths and files on the remote server. If you do not want to have separate resources for separate users, I suggest that you use a generic account user ID and password in the resource configuration for easier path and file name entry.
If you would like for GoAnywhere to look at the current task for override values which would be used to connect for the File Chooser, send an email with the case number 31724 in the subject line to: firstname.lastname@example.org. The message should indicate you would like an Enhancement Request form. Once you fill it in and return it, your request will be considered for a future release of GoAnywhere MFT.
Remember, the Server tab (SFTP Server, FTP Server) is for overrides during execution of the project, not for project setup. You are allowed to put Variables into those fields (UserID/Password) and pass that information into the Project to accommodate the use of a single project for multiple users and their defined connections at execution time.