I wouldn't call it wonky, even. Certainly the fact that any given match can present the players with situations that are wildly different from those recalled from the saga is not unique to Star Wars: The Card Game, but is a trait common to all CCGs based on an intellectual property with an overarching storyline, a group that even includes Magic: The Gathering with its annual book cycles. For an in-universe point of view, one needs to think of these games, not as retelling the events from the story in question (that'd be boring), but rather, telling a new story altogether.
When it comes to Star Wars, we are looking at an alternate saga, one in which events that might seem incompatible from a fan's perspective, might make complete sense, if one takes the time to consider how they might have occurred. Let's say, to use the example given, that Tarkin targets Hoth for destruction. This makes complete sense, if one considers the possibility that Tarkin survived the destruction of the Death Star - if indeed it was destroyed at all - and went on to lead the Empire's search for the new rebel base.
To stay on the topic of expansions set in other eras, I want to extend my point a bit further. What if a player chooses to build a DS deck that uses the following cards:
Affiliation: Separatist Confederacy
while the LS player brings the following:
Affiliation: Rebel Alliance
Well this is certainly a mess, at least from the perspective of events as they occur in the Star Wars canon. We have Luke Skywalker, who wasn't even born until the Separatists were defeated; and Maul, who wasn't alive to see his master become Emperor. We also have two revolutions going on at once: one performed by the LS, and one performed by the DS. For this to work, we'll need to broaden our scope of the game's "cinematic design" considerably, perhaps even assuming that a match between decks. And keep in mind that this is only for the purpose of describing how the juxtaposition of these elements could be explained. If one is willing to ignore the saga and just let the game play out as it will, nothing about this should hamper that.
The biggest question, I suppose, is the presence of the Rebel Alliance in a time period still populated by the Separatists. For this I recommend a deleted scene from Revenge of the Sith that I very much regard as canon, in which Mon Mothma and Bail Organa define their motives for opposing the Chancellor, emphasizing that they do not wish to leave the Republic, but preserve it,an ideal which later evolve into the formation of the Alliance to Restore the Republic. I could easily see Rebel Alliance objectives appearing in a prequel-based expansion, and the affiliation could also exist in the New Republic era, but perhaps with an affiliation that reads "New Republic" while bearing the same symbol.
In this particular match-up, Anakin never turned to the dark side, but joined his wife and the other Senators in their resistance to the newly-formed Empire. Perhaps this turn of events was brought about by Obi-Wan's death at the hands of Darth Maul, who continued to serve his master in the manipulation of various worlds and corporations into forming the Separatist Confederacy. Anakin had no one to train him, leaving his tutelage as a Jedi an open-ended scenario. When he eventually came of age, Anakin trained his son in the ways of the Force. And so on and so forth.
Again, this is just an example of how it's possible to retain the spirit of the saga, while reimagining details to reflect the cards on the table. For me, it's a fun way to look at a familiar story, but I suppose it's not for everyone, and I can certainly understand why some would not want to see cards from different eras splashed into the same deck.