Although Suzuka maybe very important in Japan, it pales in comparison to HRC's concern and ambitions of winning in MotoGP. It's like Bathurst and Formula 1.
Suzuka is less important now than it was but HRC have been a little more serious over the last few years since Yamaha started using their MotoGP riders so I suspect that it's meaning is again gaining strength.
I have no doubt that the reason they let CS ride it was because he wanted to, a bucket list type of thing and they could see benefit from it as it strengthened their team (his times were top Honda as well from memory until the stuck throttle)
You honestly think Honda declined Stoner Dani's ride for no particular reason other than "Casey deserves to be fighting for the podium rubbish he churned out to the press" what a load of complete ........ that was. When they offered him rides earlier and had no issues with it. Do you really think Honda thought Aoyama would get better results than Stoner when he finished in 11th? What was so wrong with the bike that Stoner wouldnt be able to fight for the podium on, when Marquez finished in 1st? Some times you have to read between the lines.
It was reported that HRC declined for a few reasons, including lack of test time for Stoner and concerns about his race fitness, whilst Stoner himself said he would expect a 5th place finish at best, so they (HRC) went with Aoyama (not at Stoner's behest). There was some speculation as to whether team Marquez had input in as much that they did not want CS to ride so early in the season so make of the varied stories what you choose but if HRC were unhappy that early with CS than they would have pulled him from Suzuka which they did say was important for them.
As for Aoyama, well look at this year and you may see an answer.
Other riders were available and HRC chose Aoyama did they not, so in short it has little to do with results as if they (HRC) were concerned about results they would use riders that can compete at a higher level than Aoyama (who's race pace actually shows why having a high quality test rider is critical to progress).
But reading between the lines is fraught with danger by one's own bias, perceptions, interpretations and exaggerations as well so often reading between the lines distorts the story and life is based on what happens, not what may happen if ............