"On top of that, by using such a specialized system to run your apps, you lose all the flexibility of having a full linux OS to troubleshoot and debug from. You now have to rely on them building on all the components that already exist in regular Linux world, like debuggers, tracers, sniffers, profilers, etc. You'll have to slip all that into your application deploy to troubleshoot a weird one-off bug."
CoreOS is a full fledged linux, and since applications are running in containers, there is no reason you couldn't use debugging tools on the host.
Most production services have strict controls anyway, so it isn't like it is common practice to log in to a production database server and do apt-get/yum install gdb and start banging away.