The example might not make it entirely clear, but on Windows, you need to specify the full path to Flash/Animate as well as the full path to the script you want to execute. You can omit the .exe extension, and it’s a good idea to enclose the paths in quotation marks in case they contain special characters or spaces. Example:
"C:\My CreativeCloud Installation Folder\Adobe Animate 2024\Animate.exe" "C:\My Scripts\test.jsfl" -AlwaysRunJSFL
This technique works for me. Here’s the test code inside test.jsfl:
fl.createDocument();
fl.getDocumentDOM().addNewRectangle({left:0, top:0, right:100, bottom:100}, 0);
fl.trace( "Hello, world!" );
The result is exactly as expected - a new document is created, a rectangle is drawn at the specified coordinates, and "Hello, world!" appears in the output panel.

Unfortunately, I couldn’t get the AlwaysRunJSFL parameter to work, and this dialog still appears every time the command is executed:

Thank you so much for your response. Thanks to your help, I figured out the issue. When I ran it from the command prompt, that dialog box never appeared. However, after uninstalling and reinstalling the program, the dialog box showed up. I guess I must have selected "Don't show again" by mistake. There wasn’t any option in the settings to bring it back, so reinstalling was the only solution. I really appreciate your assistance and hope this will help anyone who reads it in the future. Thanks again!