That's the downside of creating games with Honey Select
It's actually PlayHome, not Honey Select. Both are released by Illusion Soft, so everything else mentioned here still applies. Also odds are that they reused code because the studio part of Illusion games look very similar.
For this game to be released as a for sale game anywhere, the graphics would have to be made royalty free through something like Daz. This means redoing every single image and video. That could have been a realistically sized task in the early days, but not anymore. Personally I would likely have opted for Daz from the start due to the ability to provide higher quality images, but then again it has been stated that PlayHome was picked because it comes with a number of spanking animations, which is a valid argument, particularly when considering the quality goal and graphic skills during the early days. It's possible Illusion Soft would have been avoided if it had been predicted what the game would have grown into today, but multi year game developments almost always end up with learning something in the early days, which turns out to not be the best choice for how it end up. It's kind of like building a house and then want major changes after all the walls have been built. Once you are far enough in what you are doing, your path has been set.
In a way talking about changing this is like the proposal somebody came with in this thread ages ago where 3D models should be used at runtime to change clothing on the fly rather than pre-render every single image. Cool idea, but not supported by Ren'py so it would mean rewriting basically all the code and possibly all the text. Again not really a realistic workload. Also I actually quite like that it uses Ren'py for text display as it does that part quite well. Some old visual novels are awful because the VN text handling engine is outdated and awful. An awful engine results in an awful experience regardless of how good the story is.
Overall the choices made for the game are good or it wouldn't be a good game (and we all know it's a good game). The issue isn't the game, but the proposed changes people show up with late into development.
... and since Illusion shut down earlier this year even the theoretical chance of getting an agreement with the holder of the rights is gone, since nobody knows who it is.
It's a valid question if the current owner of the PlayHome IP is even aware of their ownership. It's not uncommon for bankrupt companies to be sold off in pieces where each piece is a package of multiple items. Going through every single item at an auction would take ages and would likely result in less interesting stuff having no buyers. This means somebody might have bought package A without being aware that the PlayHome IP was included in that package. There are games where nobody knows who owns them. The internet claims it's company X, but when you ask that company, the answer is that they don't know and it would cost too much for their legal department to investigate since that would cost more than they would ever make selling such an old game.