I do think that the BP team is focusing too much on the in-fluff defined role of the Hyperion as opposed to the in-campaign established appearance of the Duke. I find it highly strange that people are married to the conceptualized role of the ship, rather than letting its already-defined role which has ingrained itself in much of the audience's mind dictate how it should be directed, but that's purely opinion.
This is my understanding of the situation:
Take, by analogy, the Hyperion as an undeveloped side character in a comic which has only been featured in a prominent way once. The author/artist may have a good idea of the character's intended role or personality, want to feature them more prominently in the future - perhaps 're-using' this side character for continuity reasons, recognize a disjunct between their current appearance and the character's newly-conceptualized role, and thus be tempted to alter their appearance to suit this. They view that their plans for the story - which hasn't been yet presented, as more important that the visual appearance of the character. The readers, however, are not benefit to this knowledge - their only association to the character is their appearance. A change in the appearance would cause readers confusion.
I honestly don't give a rat's anus about what the cruiser's supposed combat abilities are, and why they should be reflected in the design in this instance because
it never prominently displays them in any way, and thus is irrelevant. You could come up with any role you want for it, because in established missions, there's very little (read: nothing) that prominently establishes what it's supposed to be doing. More important is the Duke's prominent and
visible role of something unique-looking that is the objective of an entire series of missions. This a work of fiction - the Hyperion's role is
whatever you say it is as long as it's consistent with its existing appearances and is reasonably believable (suspension of disbelief, etc). There is nothing, as far as I recall, in the Hyperion's existing appearances that clearly define its role on the battlefield, and thus I do not feel that there should be any emphasis on adhering to this supposed role when choosing to redesign the ship or not. As such, yes, any cruiser
could work just fine, and the Skaal-Tel or Stratcomm's model indeed fits the Hyperion's "role" just fine, but I'm compelled to argue for something that is recognizable to the current design, which is far more visually distinctive than the current iteration of a mini-raynor and has been clearly established in the "visual canon" of some people already.
People don't remember nor care what some random cruiser that may as well be the GTC Redshirt 11842 exploding in the background, unless it's a direct obstacle to your objectives (ie. that Aeolus that flaks you at the start of that one mission), they probably are even less attached to the statement as to the role of said cruiser in the techroom. They remember and associate far more when said cruiser is the centerpiece and focus of an entire 3-mission pursuit scene, particularly when the most memorable feature of it is it's rather distinct appearance and not anything it does in particular.
The BP team, as the dev team, have a much greater and more intricate understanding of what you want the Hyperion to be, what plans you have for it in later missions, and a far stronger conceptualization of what niche the cruiser fills in the fleet. The general public does not have the benefit of this insight and thus in the lack of prominent presented feats and stunts, tends to focus more on the visible, more "tangible" aspects - that is, for example, a shape which differs substantially from your "Standard Terran Spaceship". Thus, this argument is kind of shaded by perception bias on both sides.
In the end, it's a design choice to be made by the authors - what do they value more? Their plans, or the audience's pre-established perception of something "wrong" as though it may be. There's no reason the author should have to alter their perhaps exceptionally well-reasoned plans for the actor for the audience's perhaps misguided view of said actor. The change would surely disorient the audience, at least at first, but that may be viewed as a necessary step to align the characteristics.
tl;dr: I'm more comfortable with a skaal-tel looking hyperion but the end choice of how to go about it is the BP team's and we should respect that decision. I just don't have to like it

(just like how i don't like how the Raynor's name was changed and the tri-bar region was removed but hey, design choices)