I think your analogy would be a lot better if this was actually an in-depth or complex game. Renpy is ridiculously easy to use, and StS is basically a visual novel with some map screens and a couple minigames. People definitely can (and do) make some impressive things with Renpy, but this isn't one of them. Any halfway decent programmer could remake StS in its entirety in like 2 months tops, and that would be starting from scratch.Its not really an engine "update" its more a restructuring of the entire code base. The code DC wrote before the "update" was most likely a big pile of spaghetti code. Spaghetti code is exactly what your imagining a huge fuckin mess and it gets really hard to deal with it the bigger the project gets.
The reason its taking so long is really up in the air at this point. From my experience re structuring the whole code base is a pain in the ass and can take quite a while.
Think about it like building a house. You need to have a blueprint of what your making, you need to know what material your going to need, how much of it, where to find it and how to get it where it needs to be. Your gonna need clean the lot and compact the ground, put in a foundation and all that. What DC did before was just grab all he could an through it together. Since hes an artist it was basically a really good looking house with a shitty infrastructure.
I think that DC and/or his team are just talking about this tech update and restructuring as another way to essentially stall out having to make actually meaningful progression to the game, but I also think a lot of people here know that already as well.
Source: I've made a game in Renpy that was similar to this kind of sandbox. It's really not hard.