You're right we should add an auto-backup facility (been on the todo list for ages like a lot of stuff), I'll try and get it done sooner since two of you could've used it recently. However, you should also see best practices - back up regularly! Auto-backup is still not enough to secure your data (see the article - hardware failure, fire, floods, theft etc. can still cause disaster). Using project folders is the same, and they can still corrupt if your computer crashes/BSODs/disk skips during a save, they're not much different to .capx in that regard.
I cannot recommend enough that you keep a daily backup on Dropbox. It takes literally no time at all and even with autobackup in Construct 2, it will mean your data is safe even if your entire computer is destroyed.
In fact I think it might be worth adding a built-in feature to backup to a dropbox folder once a day. I'll try get on that for the next build.