Japanese 416 One Yen 900 - Authenticity?

Ginza is the top tier. For anything graded they will always be more expensive but on the other hand for graded stuff they tend to only buy stuff that is at the very least top 50% for the grade so often their offerings are superior to the actual grade.
Ginza is actually a bargain for filler coins because they know how to recognize cleans and issues and adjust the price respectively. I got some of the rarest varieties that way when I was first starting.

As for the pricing well my reasoning for individual sellers on ebay (it is different if it is a well known coin shop) is as follows. If you are selling your coin at HA what do you get. You get the price WITHOUT the premium minus the fees that HA charges. Now if you bought the coin at HA yourself you get a discount on their charges or it is sometimes free.
So look at it this way. You buy from HA and you basically get a coin at price X. Why would you spend the same amount on ebay where they don't guarantee the coin and they don't have experts looking at it. You wouldn't. If you bought that coin on ebay you would expect to pay less for it.
One other thing, HA would TELL you in the auction if they felt the coin was overgraded. Not directly but they would mention things like touch marks and handling and if it sounds more than it should be for the grade you can tell.
On other coins - I bought one sight unseen that I knew was MS70 even though it was ungraded because they specifically said they could not identify a single mark. It did indeed grade out as a 70.
So if you think about it why would you ever pay on ebay more than the HA price minus the premium because you get much more comfort from HA than ebay.
The only reason to buy on ebay is from the regular coin shops that also advertise on ebay and there you pay for A) the coin shop's guarantee and B) the convenience of getting exactly what you want right away rather than having to wait for an HA auction to show it.
Hence if you want an 1870 1 yen at ms65 you would probably need to wait 3 months for one of the signature auctions on HA to roll by. You could instead get one on ebay tomorrow from a top coin shop obline but you would probably have to pay up to 1k or something over the price it would come to on HA.
So yeah the fact that it is graded (assuming you do your homework to check that the graded coin is the correct one because there are TONNES of fake coins in convincing TPGC slabs) puts it closer but still the guarantee that you get from HA and coin shops is valuable.
I for example have sometimes had people try to sell on ebay rare varieties that aren't in fact that variety. Often it was misattributed by PCGS or NGC - that happens quite often. I have had people sell for example type 1 1870 1Y coins as type 2 because it was attributed as such but was obviously type 1. A coin shop or HA would catch that, the non coinshop ebay seller may not even if they are being honest.
Of course there are some sellers on ebay that are great collectors and so are virtually as reliable or more reliable than coin shops and their sales command something closer to what HA would .
At the end even with coins you get what you pay for except for that ridiculous guy who I won't name that shows "discounted" offers which are at 10X of the fair price of the coin... I have no idea why he is allowed to continue ...