I personally find Huddersfield more hostile in the evenings than Dewsbury, though I haven't been in Dewsbury since they started the rebuilding work, so maybe that makes a difference. There's definitely anti-social behaviour there, but because it's quite open and spacious and gets used as a thoroughfare to the Asda, it isn't somewhere you could get "cornered". Huddersfield feels like somewhere you could get trapped because of the lack of circulation space. The piping of classical music is clearly intended to discourage youths from loitering but it doesn't seem to work. As a result that and the loud recorded announcements just lead to sensory overload.
One thing your list says to me, is that it isn't the type or quality of building that makes the difference, but the general atmosphere of the town/area the bus station is in. Holmfirth certainly isn't a fancy building like Batley or Cleckheaton, but it's in leafy quaint Summer Wine country so there's fewer crackheads hanging about the place!
I guess it is perception and subjective. I've always felt ok in Huddersfield.
However, I think you've hit on a point. There are usually several factors at work. Design, location, and location. So yeah, the bus station at Holmfirth might not be shiny, it works because it's a nice little town and it's quite central so you have a reasonable footfall.
Conversely, Batley isn't quite a genteel, and whilst a decent bus station, the location is out on a limb somewhat and it doesn't feel that busy at most times.
Chelmsford was a combined garage/bus station, but now a reduced bus station with mixed commercial/residential
One of many places e.g. Newcastle Haymarket, Ipswich (Cattle Mkt), Gloucester, Cardiff where a bus station has been replaced by a smaller alternative.
Another of the "ambitious" ones is Merthyr Tydfil. Now the old bus station was really bad - feral kids, bad design, old and not maintained etc; a truly awful place to wait for a bus. The new one is a great improvement but you wonder about the maintenance budget. Also, and I might be misremembering, there was a coffee shop and a newsagent type kiosk in the design and neither had tenants last I was there?