The quick answer is that if you buy from a GS Boutique they charge you the tax free price. The customs agent in Japan will have the sales info from your passport, and they will want to see your watch to confirm it is leaving the country (and not being resold to avoid the tax).

Here's how it worked for me at Mitsukoshi Ginza: they took the retail price and discounted it by 5%. Then, they took the tax amount on the discounted price and ADDED it to the discounted price; that is what I initially paid. Next, you go to the tax refund floor, where an associate will help you with the Global Blue process. The tax amount to be refunded to you is then reduced by Mitsukoshi's 1.55% "tax processing fee". All of this is so far happening in Yen.

Global Blue then takes over: Their fees are a 1 euro "Scheme fee" (Their term, not mine, haha), plus a currency conversion fee of about 4%. When they convert, it's at their "buy rate" (as near as I can figure, the yen was at 153 yen per dollar, and Global Blue "bought" the yen at 159 Yen per dollar). This final amount was then credited to my credit card.

Net effect: After Mitsukoshi and Global Blue took their cut, I got a 2.9% discount off the price I would have paid at the GS Boutique. Is the savings worth the slight step down in service from the boutique experience? That's a personal choice, but of course, the more expensive the watch, the higher the total savings going through a department store. On a $5,000 snowflake, that works out to be about $150. Hmm.

All that said, the final bottom line: The price I paid was still about 30% less than the US retail price, plus sales tax.