I do not think mentioning your old landing permit sticker or not will make any difference. An officer at a passport control may not know about your travel outside of Japan unless decide to check passport pages for stamps of other countries, but as far as entry history to Japan is concerned when an office put your passport on a scanner I am guessing that the screen an officer will be looking at pretty much will show that your last entry to Japan was less than 90 days ago and other entry/exit history to Japan. I am sure every day there are so many non-Japanese passport holds entering Japan like that and I really do not think mentioning your old landing sticker or not will make any difference.

I mentioned “I am guessing” but my mom used to work for an export company before retirement and her job involved working with customs office regarding shipments. She frequently went to customs office for work and she heard some stories about what officers know about the person from the screen they are looking at, how officers typically decide which person they will inspect or not, etc.