I know for the most part we've all been able to use our cards instead of the passport sticker for tax free shopping, assorted rail passes, etc. However, the official rules for the Japan Rail Pass haven't technically allowed for it, and since Japan is generally a stickler for rules, I've frequently had a nagging feeling that one day I wouldn't be able to use my card.
Up until recently, the Japan Rail Pass website said "if you use an automated gate, no stamp will be applied to your passport. Either use a manned automated gate or ask a clerk to apply the stamp to your passport."
The website has been recently updated to show this, saying it's officially ok, starting June 1:
Now, if we can travel from June 1 or not is a completely different question...