Before these weird recent titles, I was in complete agreement with you. (On a side note, what we've done for other anthologies is not necessarily consistent.) Also, I agree with you 100% regarding Torchwood. There are many other prefixes used over the years.
I also want to agree with you on the new UNIT anthologies, the only ones that might stand out. But does it play the same role? Compare: "UNIT: The Coup" with "UNIT - Shutdown". The latter can be read as a noun phrase: "UNIT shutdown" (like school shutdown). The former cannot possibly be read this way. All of the new titles can form a meaningful phrase if the dash is omitted (it is a dash on the website but just a linebreak on the CD box): UNIT extinction, UNIT shutdown, UNIT silenced, etc. I think it would be wrong to pretend that nothing is changed.
On the other hand, this change is so subtle and, seemingly, far from being decisive in the title. It's an additional flavour to the title, an aftertaste, not the main attraction at all. So perhaps, we can still omit the prefix without losing much.