Well, what you mentioned could open some discussion regarding how to model scenes...
When I started to model for TA, the goal was pretty much to make the scenes HD, and try to exactly replicate how it used to be in the original. My point of view has significantly changed since then. It turns out that if you try to simply upscale a scene as you remodel it, it just doesn't work fine. The main reason is a problem of scale. Many items in the original images were scaled in such a way to make them recognizable at the very poor resolution we had on PS1 era games. But if you keep things at the same proportions as the original and make it HD, it just looks dumb. For instance, the original scale of the tea cup in the item shop scene is 38 cm in diameter and 40 cm tall. When something looks absurd, there's no saving it on the reason that "it's set in a fantasy world anyway". For having believable environment, it's important for us to correct all these clunky details as we remodel things.
Additionally, as we remodel things in HD, we have the ability to bring in lots more details which also contribute to make the world more believable. I disagree strongly with the simplistic idea of enhanced graphics being detrimental to story-telling: if anything, enhanced visuals can tell more without a word. For example, in The Last of Us, just when entering random houses, you could start imagining what kind of people were living there, and recreate their lifestyle, just with the amount of details given to the environments.
All in all, when we remodel a scene, we have to interpret the original, and build something coherent from there. In the particular example of the 5min1_1 scene, after I decided to go for the old tatami floorings, I sized tatami according to the traditional Japanese standards. I laid out the tatamis according to the rules for auspicious arrangements, I don't think Japanese people would have done otherwise. Then, to keep all the tatami together in the area filled with clunky pipes, I either cut out some of the tatamis to have enough gaps for these pipes, or I inserted pieces of plywood like a slum resident would for an easy and cheap fix. If I had tried to exactly replicate the original, I would have ended up with oversized, awkwardly shaped tatamis, and I don't think that would have worked better. Don't get me wrong, I want to be respectful and faithful to the original design, but I want to work on ways to improve it, when it is possible. It is also the main advantage of our HD remake of field scenes over the "enlarge and photoshop filter" method you have in Omzy's graphical overhaul.