I think it's like a lot of Customs regulations in many countries: it's based somewhat on the honor system, with a fallback that they do detailed inspections upon suspicion and/or at random, and you're in deep doo-doo if caught in a lie. More to the point: during a Customs inspection, you almost always are forced to make a declaration to the officer before they actually uncover the contraband. So, you get caught not only with the contraband, but in the lie.

For example, let's say you're selected at random at Narita for detailed inspection. You confirm to the Customs officer that you indeed have everything listed on your tax-free export forms with you or in your checked bags, and for consumables, in an unconsumed fashion. You might actually sign something to that effect. Then they pull your bags and find out that you lied. Perhaps you're in big trouble at this point.

Note that it's not that this happens regularly, but the notion that it can happen will keep most people honest. That, plus there's the rather simple notion that you were given a special privilege as a guest to the country, and it would be nothing short of rude to actively try to circumvent the rules in order to save 5% on the shampoo you bought locally and used during the trip. And, if you bought something on behalf of a local in order to evade the tax, you certainly have nothing to complain about if you get caught.

My guess would be that if you ever had to present your effects to a Customs agent to verify you were exporting the goods that were sold to you tax free, that even if the sealed bag were broken, if you nonetheless had all of the described items with you and in an unused state, it would take no more than an apology to resolve. Although officials charged with enforcement duties such as these definitely don't like people breaking seals they're not supposed to be breaking, their primary mission is to catch tax evaders.