For those who are interested, the following is my experience of obtaining a Spouse visa through a Consulate of Japan in San Francisco, USA:
TL;DR
The visa was granted within five days from the submission of my documents and my passport was ready for a pickup after that.
DETAILS:
I have applied for a Spouse visa at Consulate using the non-CoE route, as outlined on the following page:
https://www.sf.us.emb-japan.go.jp/itpr_en/e_m02_01_03.html . It seems that the non-CoE route is available in San Francisco only. I checked the Spouse visa requirements for people residing in other big cities in the US (Seattle, LA, Chicago, New York, Atlanta, Portland, Houston) and the Consulates in the aforementioned cities do require an CoE. I have no idea why applications in San Francisco are treated differently.
The submission of the documents was pretty straight forward. The Consular officer collected all the documents that I was suppose to bring by carefully inspecting each of them as he was collecting them from me. His biggest point of interest was to make sure that I have my wife's koseki. In addition to koseki, we also provided our foreign marriage certificate (although it was not a requirement as outlined on the aforementioned Consulate page). He did ask though if I have my wife's Japanese passport copy (this was also not an outlined requirement), which luckily I did have, so he took that as well.
In addition to my bank statements, I also brought my salary payslips. He collected only the latest bank statement, plus the latest payslip. To note, to bring my salary payslips was not a requirement, but I had them with me just in case.
In terms of a verbal communication, the officer did not ask me anything unusual/tricky, all the questions were pretty straight forward (he was very friendly and kind): how long do I want to stay in Japan, when do I want to fly out, which airline I will be flying with, what airport do I want to land, who will pick me up, where will I quarantine upon arrival.
I was not asked to provide any proof that our pre-marriage relationship is/was valid & genuine. I asked the officer if he need the proof/documents and he said no. I brought enough evidence with me (emails, photos, chronological description of our relationship letter, etc.).
Since I was asked to come back to pick up my passport after five days, it suggested to me that my application was not mailed back to Japan to MOFA/MOJ for verifications of any sort.