What are you talking about? This is the BEST way, bar none, that I've seen for this development model. Incremental releases that don't require you to download the whole damn thing over and over again with each new update, no "we changed something so your saves won't work and you'll have to start over at the beginning" bullshit. The only other one found here, (that I've played, anyway,) that comes close to being as sensible a release model as this is "Glassix", with its update patches. A lot of devs could learn from the example of these two games.
Plenty of games manage not to break previous saves in a single game file, and it could just as easily have been fucked up with this release model. The reason it isn't is that previous saves have largely no effect on the story, not that the chapters are individual programs.
And this means you cannot replay previous chapters without quitting and starting up the previous chapters, you can't change a previous decision and skip ahead to a further point without problems (again, not a problem for this game where choices don't matter, but that would be fatal for most other games).
Literally the only argument against single-executable games is a large download size, which is a very weak argument, as a) there are almost always compressed releases available and b) even assuming you have a shitty connection... so what. You waited a month for a new version, can't wait another hour or two to download it? And if you have a fast connection, it's just another few minutes...
And not to mention that setting up incremental downloads would also be possible for single-executable games, if people cared to do it. Most developers don't, and as a consumer, neither do I.
Tl;dr, this release model is very annoying. But there will be a single game in the end, apparently, so it's only annoying for those among us who can't wait that long. And for this game in particular, I can put up with it.
A bigger issue is that it's not Ren'Py. The game controls are just awful. But that's another story...