It doesn't matter that it isn't Chase's story - he's still a character within it. Characters beyond the main ones can develop and have focus and they certainly should be written well and not treated simply as tools for the main cast. If the end result of everything that has happened up to now was that Chase was just going to magically get reset and go back to how he was before Heart got to him, as if he had never been the "Grim Reaper" and never defended Roidmudes, then they honestly might as well have captured him before Gou showed up and reprogrammed him for all the point any of this actually had.
Certainly, Shinnosuke had to deal with killing him and Kiriko had to deal with helping him while he was a potential threat, but neither of those things really had any impact in the long run because now he's back and on their side and nothing was ever really done with either of those things. At best, we got some minor filler plot out of it, but nothing really substantial for their character - the conflict between Gou and Kiriko would still be present if they'd skipped that because you still have their conflicting feelings for Chase.
Also, the problem is that what you're saying all hinges on the fact that Chase is a robot and there's this implied magical mind control with the programming going on here. If he were a purely sentient being, like a Fangire or an Orphenoch or even a Phantom, this would be unquestionably shallow writing. In the early part of the story, he was under Heart's control until he started remembering things, and thus began his conflict - this was before Gou even showed up. When he was freed of the control placed on him (by Medic at that point I think), while still wanting to defeat the Kamen Rider, he clearly was upset that the methods he was using against his will were not his preferred ones - this pretty clearly implied that he was not just a tool, up to that point, or if he was, he still had some kind of person within it. Did that person just cease to exist now? And is it okay to accept that "because he's a robot"?
When Medic really started screwing with things, this definitely became blurrier, but after his "death," it looked like he was, again, conflicted about what he wanted to do, and in this episode, we even saw a little of that with how he defended Heart. Prior to it, he was sticking to himself and trying to sort things out, avoiding both Kiriko and Heart - clear signs of a conflicted character.
The fact that he can just turn around after everything we'd witnessed to now, regardless of whether or not it makes sense or whether or not it's "his story," is just poor writing. If all of that early in was to simply establish that Chase was an "honorable" Roidmude or to foreshadow a little who he was, they didn't need to make him so invested. If this is all simply an issue of being able to cheat character development by having a character you can freely change at will, then him taking issue with his reprogramming and him even being considered a character in the first place doesn't really make sense. Chase not being conflicted about this proves he doesn't have agency. Because what is he doing now? No different than what he's done before. All he's done is, at best, get reset back to his original programming, even if not literally.
I suppose in that respect, you are right that it's not his story, because he's essentially just a walking plot device at this point.
I'm not saying I have a problem with this being how he ends up, but for him to just end up hear without any contemplation or issues about it, it really does feel like it's just something they rushed to start selling his new weapon on time. If they'd given it maybe one more episode for him to decide and come to terms with it, maybe that would be something else, but for him to go from the character he was in the start of this episode to the one in the end with what little meat there really was in-between is just... disappointing, really.
