The flag console is there not to cheat but to fix bugs that might appear to break the game (if you check old posts you might find people encountering bugs like these), for example on version 0.8.4 during Amy's path there was a bug that made the game loop after having a drink with her than riding the taxi with Veronica so you couldn't continue. The only way to fix it at that moment was using the flag console.
Also, people tend to think that the game is broken when they screw up. You place the stat cheat and instead of increasing the value by 4 then getting the last one the proper way like you described I'm sure they would increase it to max then start complaining if the game broke. The flag console is different in that if you look at it, without any knowledge, you have no idea what it will do to the game (the first time I saw it I immediately gave up on messing with it). I found the game when version 0.8.3 was being done and compared to then (when the stat cheat was a thing) I don't see a lot of people trying to use the flag console to cheat compared to the stat cheat then complaining that it broke the game.
The game was designed with doing multiple girls at once, so while I agree that waiting for a Sunday event to advance on certain girls path is annoying you can just pass the time with another girl. Also, the grind was greatly reduced and now you can do like 2 or 3 events to increase the stats at a given moment. For example, on Emma, you can either increase her AROUSAL stat by doing the beach event 5 times (need 5 weeks) or visiting her at the massage room (need 5 days).