1. itch.io uses PayPal. Assuming you trust them, there is nothing to worry about.

2. itch.io provides the same mechanism. You are paying for the game, not the single download.

3. As long as you can re-download the game, then there is no reason to save the installer. Serials/keys are up to the discretion of the game developer and I don't see why giving the game developers control is a bad thing. I think most indie games are against DRM anyway.

4. In order to support auto-updates, the game developer has to invest in the Steam APIs. There is nothing stopping games on itch.io to using out-of-band updates.