I feel like the answer is twofold.

Either the developers hit technical limitations of their save system and couldn't reliably restart everything. I feel like RDR2 did this because most of their missions were very specific scripted sequences that needed to be kept on track from the start. A lot of roguelikes are unable to save during a run or within a node of that run. For example Peglin and Void Bastards. It's much easier to say what node or position the player is at than all the AI states, combat, etc. Additionally, automatic saving has always been difficult. Everyone knows the whole "the game auto-saved and now I die instantly over and over again" bug that happens in any game. The way to negate this is to use checkpoints with areas where you know the player isn't going to get attacked. Another way is to try to detect when you are in combat or not but this can lead to the game never saving. Overall it's much easier to just save a state that you know the player will be okay to start back up in.

Or the designers felt like it added something to the game like in Alien Isolation. Save points allow you to exit and designers are trying to focus on keeping players playing. So save points are also an exit point. When you allow the player to save, you allow the player to exit without feeling like they must continue going. Designers use this to try to keep their games more engaging. Super Meat Boy removed a few exit points from typical platformers in order to make the game faster. A lot of games try to be so easy to keep playing that they make it hard to stop. In some ways, this can be seen as a dark pattern in game design. Typically though, designers aren't trying to be nefarious but instead trying to keep the game engaging.