For many games, there are so many variables, options, statuses, etc., that it would be impossible to do that without just giving a generic save that may not have everything you want in it, or giving 20 saves to accomodate all the available pathways... it would just become a logistical nightmare. This game may not be quite in that bracket, but there are still scores to consider and some choices that will determine some of what you continue seeing later in the game, etc.
Also, this is just a generalisation, anyway, right? All the message here said was that due to a Ren'Py change/issue, auto saves won't work, but manual/quick saves still will. So not the dev breaking the save at all, and also no problem to actually be worried about here, unless you only use auto saves (which is surely not something people actually do, is it?).