Visa stamp vs visit japan web qr code

Hi, on the guidelines for redeeming/activating the JR pass it is mentioned that it is necessary to show the customs stamp for tourist visa on the passport. I have a question regarding that point:

• As I’m from Portugal and have a Portuguese passport I have visa exemption for stays up to 90 days so technically I won’t have a “visa”. (I’m just staying in Japan for a normal 15 day vacation) Also, I was considering using the Visit Japan Web QR code and not go through the manual customs, which I guess really means there will be no stamp whatsoever on my passport, I’ll just have the qr code on my phone.

So can I still redeem/validate my jr regional pass with the qr code from Visit Japan Web? Or do I have to go through the traditional customs and get my passport stamped?

Thank you