So my entirely non-expert opinion of those reasonst is - lame.
True, it is obvious they don't care about B5, which is frustrating when there are people like us, who would be willing to watch HD versions and buy Blu-rays and merchandise, who do care.
I think, from what I can glean from listening to people in the know talk about licensing details with places like WB, is there's a lot more that goes into licensing than appears from the outside. For instance, WB do of course have a licensing department, but probably no one on staff who knows Babylon 5 (in that podcast, when Ben Robinson says he inquired at Universal about the old 70s Buck Rogers series, the people in licensing didn't even know Universal had done a Buck Rogers series). There needs to be someone who knows the show because, let's say they gave the rights to Eaglemoss to make models, for example, and Eaglemoss got the designs all wrong, there needs to be someone at licensing who knows they've got it wrong. Artwork has to be authorised and checked. Speciality soundtrack CD labels, for example, can take years to get certain titles produced because they are waiting for the artwork on the cover to be signed off by someone at the film studio. Often they sign deals with the studio to release a lot of their soundtracks, but when it comes to some obscure 1960s film, sometimes it's not clear who owns the assets, it might be no one currently in the licensing department knows about that film, or where the records are kept, and it just takes ages. I imagine WB's properties are split up among their licensing staff who have detailed knowledge of the various shows and films that they are working on, mostly current or evergreen things like Bugs Bunny; they'd have to train someone up to work on licensing B5, and who is going to train them? This might be why in the early 2000s WB said they were not going to license B5 anymore – the money they were making off it might have dropped below a threshold, and they either let licensing staff go who previously worked on B5, or moved them on to other things, and over time the knowledge of the series, from a licensing perspective, was lost.
Then there's the legal stuff – and all I can presume is that lawyers must be charging a fortune to go through contracts – but if WB were to franchise the series out to Eaglemoss and whoever, then there's probably a whole load of people they need to pay royalties to, starting with JMS, but probably other people too involved too, maybe Foundation Imaging, maybe actors if their likeness is being used, etc etc. For a modern, 'live' franchise this is probably already taken care of; I think for something like B5, it just seems like too much hard work for WB to resuscitate its licensing versus how much they'll actually earn. And since no one at the top of WB seems to care for the show, there's no one from the top asking for licensing to spend time on it.