Containers on Mac rely on virtualization, don't they still? Will the new CPU arch have a native virtualization SW? Because if not, I suspect that the virtualization layer might break with the translations to and from X86, and/or might take pretty significant performance penalty.
A wild unsubstantiated guess of course, at this point (or rather, a worry of mine).
Containers on Mac still rely on virtualization, but Apple said at WWDC (and showed a demo) of Docker for Mac running on Apple Silicon, and of Parallels running a full Debian VM. Both were running ARM builds of Linux to run properly, and Apple added virtualization extensions to the new SoC so it doesn't have to resort to emulation (if the software running is ARM and not x86).