As far as some of the issues you raised like battery replacement, I would treat them as disposable. In the next few years a complete computer will be available for so little that we will consider it disposable. Prepare a server once, enclose it, make sure the only way in or out is an SSH connection. When it's time to set up a clone to replace it, clone everything via an SSH session and trash the first server.
That could work, but the advantage of an HSM is that the key material is physically prevented from leaving the device, barring acid/x-rays/other attacks. All encryption happens on the device itself. With an open ssh connection you could still remove the key material from computer.
As far as some of the issues you raised like battery replacement, I would treat them as disposable. In the next few years a complete computer will be available for so little that we will consider it disposable. Prepare a server once, enclose it, make sure the only way in or out is an SSH connection. When it's time to set up a clone to replace it, clone everything via an SSH session and trash the first server.