I cannot explain what the designers were thinking when they selected deities for the Twilight Domain, but the theme I took away from it was protection. The Twilight part does not necessarily refer to night, but can also refer to shadow or the dangerous unknown.
All of the deities listed for the domain, to my knowledge at least, have a major protective aspect to their portfolios. So, the benevolent night/shade deities automatically fit, the sun deities that create shade as part of their light and are not all about being bright and shiny fit in (perhaps the weakest part, but can be massaged) and then the general protective deities are there. I saw no issues with Helm, as he is all about protecting the common folk, and when are they most under threat? That is arguably at night. Yondalla also has a major protective aspect to her portfolio. She really is the Halfling deity. She is all about protecting her flock, and again, it is times of darkness (figurative and literal) that they are most in danger.
I agree that this is a bit more disjointed domain than many we have seen. It really is more about "Protection" than just twilight/night. Kind of a combination of various AU field tests, as they did send out a Protection domain in AU a few years back before Xanathar's was released.
Take it for what it is worth. I am sure others will have opinions.
I know that I have grabbed the domain for three different deities in my home-brew world due to the flavour and content. Still considering if I will associate it with a fourth deity.
Cheers
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