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> 1. I run a malware as root which modifies my image. I don't run anything as root except apt. So this is impossible.

1. What if apt is compromised?

2. What if apt installs something which is compromised?

3. What if you run something which is compromised and escalates privilege?

> 1. What if apt is compromised?

Then fix it.

> 2. What if apt installs something which is compromised?

This implies apt is compromised. Goto above.

> 3. What if you run something which is compromised and escalates privilege?

If something is able to escalate privilege that's a kernel bug of the highest order and must be fixed asap.

I'm guessing defense in depth is a foreign concept to you?