This dialog is inside the generated HTML file. You find it at the end of the file. Its purpose is only to remind first-time command line users to allow file access. But it seems the warning timeout of 2s (2000ms) is too short.
Solution: You can manually increase the timeout from 2000 to e. g. 20000 and it should never show up. Or simply remove the alert part completely from the html source code:
var timer = setTimeout(function () {
alert("Error: It seems you need to enable File Access for Kantu in the extension settings.")
}, 2000)