There are plenty of Ren'Py games that never suffer from broken saves. As I understand it - 'though I may be wrong - the way you break saves is when you make changes to the game that are implemented prior in the game to the save in question, i.e. if you make alterations to the v0.6 code as you are making v0.10, (like adding a new variable retroactively or removing a character, etc.,) then saves created after that point in v0.6 thru 0.9 will likely be broken and not useable in v0.10. Yes, some may work to a point or may work with numerous errors but the way to make sure they keep working is to not make changes to old code when adding new version code.
The "Chapter Select" thing, well, I screwed up there. As I said, I last played v0.9. When I opened the "Chapter Select" menu I only saw chapters 1-6: probably because I was so annoyed by the saves issue and the need to be in that menu at all I never noticed there was another page to it. I just went first to chapter 5 then, upon discovering it was so far back in the game I went to chapter 6. I didn't notice there were more so I could've gone deeper into the game to start. That's my bad. Still, while the chapter thing somewhat mitigates the problem it still can't put you back where you were with all the decisions you made through your play. You only get to choose fully one path or the other. I know I had significant points built up in each. If your previous decisions don't matter at all it's OK to jump in at any point but if they do matter you're stuck with having to either start over at the beginning and hope you make the same decisions you did before or just say "to Hell with this!" and shitcan the game. I'll choose the latter, almost every time.
I've never played "Summertime Saga" and if they regularly break their saves I can see I've missed nothing but aggravation and wasted time. As for their disclaimer, all I would tell them is "Then either you don't know what you're doing or you should be using another engine. If you don't know what you're doing, don't blame it on the engine. If the engine's the problem, quit using it and switch to something that works right." (From the number of Ren'Py games that never have this problem I would tend to suspect the former over the latter.)