Needs some help here with determining if this disconnect switch on the stand generator panel is now the service disconnect or not? If it is then it makes the interior panel a remote (sub) panel?
It looks like it is as it say service disconnect on the ATS and there is a 4-wire feeder to the sub-panel. The sub needs the EGC’s and neutrals separate.
I agree. Bonding is at the ATS. 4-wire required to the panel.
Good catch, especially considering that green sticker on the ATS.
I took a closer look at the green inspection sticker. It’s dated 2014. The house was built in 2013 so this stand by generator was added after the electrical service was in the house. The generator may of been inspected but they never rewired the original service panel as a remote panel. Do I have that right?
Probably, but it really doesn’t matter since it needs correction. 
I think so, it is possible that they just removed the old 3-wire SEU cable and replaced it with the 4-wire SER and never reconfigured the EGC’s and neutrals in the panel on separate buses.
Also it appears that the GEC for the grounding electrode system is still terminated in the sub-panel (large black conductor entering from the bottom left) that needs to be moved the the service disconnect which is now the ATS.
Built in 2013 I doubt it ever had a 3 wire installed. I would check to see if the tag was cut. The generator may have been a moonlight install. The original panel was all the house ever had and now it to be corrected.
It appears that the ATS was added after the original inspection. Originally they would have 3-wire SEU cable between the panel and the meter otherwise why would you run 4-wire SER cable to the panel from the meter and then connect the neutrals and EGC’s on the same bus? And how would that even pass inspection?
Me bad. That would be true. I was thinking of something different