If you're comfortable using a command line, you can just use tesseract directly for this use case rather than trying to do it through NAPS2.
It sounds like you're talking about the UI provided by your scanner manufacturer, which has nothing to do with NAPS2. In your NAPS2 profile settings you should be able to select "Use predefined settings" instead of "Use native UI" to skip it, but otherwise it's based on your scanner's driver.
You'll need to click the image to select it, then you can use the menu.
You can also try "Document Correction" under the Image menu.
You can also scan in either color or grayscale, then after the scan, under the "Image" menu, click "Black and White" to convert to pure black & white for a small file size. This window will let you pick the exact white/black threshold and preview the results to make sure it's right.
Escl: Fix CORS for OPTIONS request
Worker: Fix debug logging flag
Sane: Allow getting and setting inactive options