My Canadian IDP has a little stamp indicating it was issued from the proper agency (in my case, BCAA)- I guess there's nothing stopping someone from stealing that little stamp and making their own.
However in my experience with rental agencies in Japan they ask for both my proper license and the associated IDP.

Without seeing a picture of what you're talking about I can't say for sure what it is, but I suspect it to be the VICS/ITS scanners- the traffic information system that gathers data to send to navi systems and the big traffic billboards.

I'm not too familiar with ETC, but I believe it only bills at the designated toll booths (though I would not be surprised if they scanned for ETC-equipped vehicle along major roads for additional data for ITS). I imagine it'd be quite difficult to bill cars without an ETC card inserted if they billed cars at locations without toll booths.