For starters, it was a bit unpredictable. The boss had a lot more screen time throughout the story, which always screams "1st male lead" and is probably the reason why a lot of people seem to sympathize with him more.
Even so, I think it shouldn't have ended any other way. Considering the way the chief treated Luda when they were trying to stop the time loop, there's no way she would've ended up falling for him. He only stopped being a jerk after she died, and even then I'm still not entirely convinced he truly changed. Yes, he learned how to not treat people like trash, but he probably still believes most of the crap he used to say.
I think it's funny how a lot of people complain that women never go for the nice guy, but when they finally see it happen they find a way to complain about it too

This is far from being a NTR. Actually, it would've been exactly that only if the ending had been different. She was never in a relationship with the chief, it was all a fabrication from his narcissistic mind. If this had been a trashy NTR hentai, Luda would've definitely ended up with the middle-aged dude that treats her like trash instead of the good guy.
Just because the chief had more screen time it doesn't mean he deserved Luda or that their relationship had more value compared to her relationship with assistant Kang. Even if assistant Kang might be considered "bland" for shoujo standards, he's the realistic choice that any self-respecting, sensible woman would make in real life. And even if assistant Kang was removed from the story, I think she still wouldn't have ended with the chief. She simply hated him way too much.
However, if the author had managed to fit in another love interest for the
reformed chief without it feeling too forced I wouldn't have complained as long as it was established that he'd actually treat her right.