I agree with you, the layout at ATH is particularly bad. It's even more frustrating going Schengen to non-Schengen where you might clear Greek security, then have to re-clear it at ATH because you're forced landside on the connection. Schengen was supposed to establish a common security standard such that it wasn't necessary to re-clear. That just doesn't work at ATH because they've chosen to not provide a route where you pass through the border only and never leave the secure airside area.

However, unfortunately your assumption that in most cases connections can be trusted isn't correct. Schengen member states can choose not to trust any non-Schengen security process. EU members who are not within Schengen can choose not to trust anyone's security. The UK government never trusted anyone, including the Republic of Ireland with whom they form a Common Travel Area, and wherever you arrived from outside the UK you had to re-clear. In my experience, most EU countries require you to re-clear if arriving from outside Schengen.

I'm not sure if the re-screen is a Greek government requirement, or a consequence of the layout of ATH. The knowledgeable Athens diaspora here will educate us.