Here are some of my reactions to the new rules, based on my understanding:

1. It seems like a way to send money to Japanese travel agencies. I have never purchased any sort of package from a travel agency, nor do I intend to do so now.

2. To the extent that a travel agent is involved, I would not to expect to earn points and elite night credits from most hotel chains. Nor would I expect any elite benefits.

3. It's unclear that award bookings would work. My guess is that if you want to DIY for hotels and flights, but have a travel agency in Japan take responsibility for you, they would want to collect a commission on your hotel booking. Hence award nights, certs, and some special/contract rate plans wouldn't work. <speculation>

4. If everyone is forced to go through a travel agent, will there be much price competition, or will the travel agents simply offer essentially rack rates? I don't know how competitive travel agents are in Japan (their tours seem pricey to me, and often different agents offer the same tours for the same prices with only very minor variations). There might be some cheap small ones, but it could be difficult to use them if you don't know Japanese. Or maybe many of the small ones will decide that they don't want to deal with foreigners and the evolving red tape of this scheme.

5. If communication with the travel agent is not through a website that confirms arrangements instantly, I would predict that flights and rates you want could sell out while you're waiting for an email exchange. I'd also be concerned about the typical tour contract saying that they can change hotels, dates and locations, etc. at their discretion and without recourse.

6. It's still not clear (to me) what happens if a tourist or other visitor to Japan becomes ill or tests positive? Would an asymptomatic or mildly ill person be forced into a local hospital or quarantine center? Most medical evacuation insurance will cover transportation out of the country only if you're severely ill and require treatment elsewhere.

7. If the travel agent arranges flights, they might give you combinations of bulk/unpublished fares, codeshares, and ticket stock that you don't want and can't upgrade or claim FF credit for. If there are cancellations and schedule changes, you're forced to deal with the travel agent. Hard no for me.