Even by the generous standards of Mitakihara City architecture and interior design, Homura's apartment is weird. Pure white space, floating holographic portraits hovering in mid-air, the swaying silhouette of a pendulum, the modernist furniture which takes the shape of a clock when viewed from above.... Maybe I'm projecting, but I have to wonder if Kyouko is thinking the same thing I am: "Damn, bitch, you live like this?"
Note the hourglass on the table in the first shot, hahaha, just in case you thought the decor could not possibly have more thematic symbolism packed into it.
While Madoka Magica is no stranger to surrealism, the most extreme versions - animated by Inu Curry - are reserved for the witches' labyrinths. This is not to say there is nothing unusual or fantastical drawn in a more realistic style, just that with the exception of Walpurgisnacht, most of the other instances have a kind of plausible deniability, in that while they are contrived and thematically appropriate, they are the kinds of things that can realistically exist (and in many cases, are based on real-life architecture from our own world).
It might be weird, for instance, that Madoka's house has so many chairs or such a glass-centric modernist design, but it's not impossible that such a thing could exist. Homura's apartment is an extreme example, and seems to require a futuristic technology that doesn't exist in most homes, but it manages to be just plausible enough... right up until a certain moment upends the scales.
On several occasions, the portraits shift from showing Homura's research about Walpurgisnacht to scenes from her life which the audience has just witnessed via flashbacks. How is that even possible in-universe?
Two shots from the same scene in Eternal, in which Kyubey explains to Homura that she's unintentionally boosted Madoka's karmic destiny via time travel.
A later scene in Eternal as Homura confesses her secret to Madoka.
Many people have used this scene as evidence that magical girls can control or change their environment to a certain extent, creating labyrinth-like spaces or "demesnes". This is an extrapolation, of course, but there's nothing explicitly in canon that proves or disproves it one way or the other, and it would certainly explain how Homura's environment is responsive to her thoughts and emotions in ways that wouldn't be normally possible. After all, the only other place where this happens is labyrinth, and Homura isn't a witch, so it can't possibly be a labyrinth... right?
However, if you're intent on reading this flickering as something that genuinely happens in-universe via magical means or as an indication of reality manipulation, I wouldn't necessarily stop at the borders of Homura's apartment. Given the sheer wonkiness of the architecture and geography of Mitakihara, the entire city behaves like a labyrinth - no different on the surface than the one Homura cooks up in Rebellion - or a play staged specifically for the audience to watch. Homura's apartment isn't special in this regard, just a place where the facade (if there is one) begins to slip.
But I'll admit that my primary reading of this scene isn't literal, it's symbolic, and that this flickering of memories isn't necessarily something the characters within the story can perceive or understand. Instead, like the witches' names spelled out in runes, it exists for the audience - its purpose is to a) provide visual interest, and b) show us something about Homura's mental and emotional states in these moments.
In fact, I'll go one step further and say that it's not just the portraits - everything in Homura's entire apartment tells us something important about her mental and emotional state. In a very real sense, when we are in the apartment, we are inside Homura's head and seeing the world through her eyes - more specifically, her single-minded focus on her mission (to defeat Walpurgisnacht and save Madoka), as well as how she is "haunted" by her quest and the trauma that spawned it. The "flickers" in the portraits are where we see her cold emotionless facade is broken (even if she doesn't show it otherwise when Kyubey is present).
Even in the flashbacks, Homura's apartment in earlier timelines isn't much better - it's dark and shadowy, because Homura herself is in the dark about a lot of things, with Homura lit by a single lamp and focused completely on the task at hand. From there, the blinding white space of later timelines is a natural progression, as Homura's goals spiral outward from building homemade bombs to trying to defy fate itself. Her apartment is now shaped like a clock to show she no longer has any semblance of a life outside her loops and she lives in a empty void without any softness, and or comfort, dominated by the ever-present awareness of time and impending doom.
Unlike Revolutionary Girl Utena, which has so much surrealism that it's difficult to impossible to read certain scenes 100% literally, Madoka Magica offers an in-universe explanation for the most extreme examples and plausible deniability for the minor oddities, making it tempting to explain everything literally. Most of the time, this works well enough, but Homura's apartment is one instance where this approach runs into difficulties.
Personally, I love how the backgrounds and landscapes mirror what is happening with the characters, and consider it be one of the show's greatest features rather than a plot hole, but I can see how it could be disorienting if you're coming in with different assumptions.
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