By not taking a flight from Europe that arrives in the early morning!

I guess that not being able to sleep will crack the jet-lag, cold turkey style. But if you could nap like 6 am to 9 or 10 am then it would be the best option for such an arrival. But make sure that you get up!

I don't think any hotel anywhere could charge you for an early arrival. If you want it guaranteed then pay for an extra night; that's standard. I suppose a hotel that has a day rate could charge you for that; that's an airport type thing, however.

But Japanese hotels are indeed inflexible, so they might not let you just because check-in starts at 14:00. I have no idea but it wouldn't surprise me.