How to create a new sub folder under my Pro Tools session folder with a template name

Instead of this line:

 sf.system.exec({ commandLine: `open "${newDirectory}"` });

Try using this - and fill in the coordinates and size accordingly:

sf.appleScript.finder.open(newDirectory);
sf.ui.finder.appActivateMainWindow();
sf.ui.finder.windows.first.windowMove({
    position: { x: 0, y: 0 },
    size: { x: 1920, y: 400 },
});

It seems like a short wait was needed before the "Save" dialog opened;

Let me know if this works for you;

function saveSessionAsNewVersion() {
    //First save the current version
    sf.ui.proTools.getMenuItem('File', 'Save').elementClick({}, function () { }); //can be disabled

    //Get our filename without extension
    var fileNameWithoutExtension = sf.ui.proTools.mainWindow.invalidate().sessionPath.split('/').slice(-1)[0].split('.').slice(0, -1).join('.');

    //Create a new name (get the name and suffixed number - if your session name was 'My Session 42' then save 'My Session ' in grps[1] and '42' in grps[2])
    var grps = fileNameWithoutExtension.match(/^(.+?)(\d+)$/);

    //Construct a new name based on the prefix + MIX_V1
    var newName = (fileNameWithoutExtension) + '_MIX_V1.ptx';

    //Invoke File Save As.
    sf.ui.proTools.getMenuItem('File', 'Save As...').elementClick();

    sf.wait({intervalMs:200});

    //Wait for the Save dialog to appear
    var dlg = sf.ui.proTools.windows.whoseTitle.is('Save').waitFor().element;

    //Enter the new name
    dlg.textFields.first.value.value = newName;

    //Click Save
    dlg.buttons.whoseTitle.is('Save').first.elementClick();
}

function moveFileToOldSessions(path) {
    var oldSessionsDir = path.split('/').slice(0, -1).join('/') + '/Old Sessions';
    var filename = path.split('/').slice(-1)[0];

    //Make sure "Old Sessions" dir exists
    sf.file.directoryCreate({
        path: oldSessionsDir,
    });

    //Move file there
    sf.file.move({
        sourcePath: path,
        destinationPath: oldSessionsDir + '/' + filename,
    });
}

sf.ui.proTools.mainWindow.invalidate();
var oldSessionPath = sf.ui.proTools.mainWindow.sessionPath;

saveSessionAsNewVersion();

sf.wait({ intervalMs: 1000 });

moveFileToOldSessions(oldSessionPath);

var sessionPath = sf.ui.proTools.mainWindow.invalidate().sessionPath;
var sessionDir = sessionPath.split('/').slice(0, -1).join('/');
var sessionName = sessionPath.split('/').slice(-1)[0].split('.').slice(0, -1).join('.');
var mixesDir = `${sessionDir}/Bounced Files/${sessionName}_MIXES AND STEMS`;

//Make sure the mixes directory exists
sf.file.directoryCreate({
    path: mixesDir,
});