1) security. Container breakouts are much more common than VM breakouts
2) compatibility - the Android kernel is known to be heavily modified and Debian may benefit from being run on a more vanilla kernel as it does on desktop/server
For starters, the microkernel like driver model, where classical Linux drivers are considered legacy, since Android 8 all modern drivers run on their own processes (Java or C++) and talk with the kernel via Android IPC, known as Binderized HAL.
Processes are sandboxed, in which app gets its own user id, everything that Google considers not a public API gets blacklisted, via a mix of LinuxSE and seccomp.
Native executables are not allowed per se on userspace, native code outside system processes has to always be a shared object loaded into the Zygote process fork, which takes the init role on Android. There are ways to launch executables, but they are frowned upon.
TIL that binderfs is a mainline kernel feature now,
Back when I used Waydroid, I had to use an out-of-tree module picked from the Anbox project. I have stopped using Waydroid but good to know that binderfs is a thing!
Containers are native executables (with cgroup rules sprinkled on top). If Android does not let you call exec in the traditional way then you have a problem.
Also you're moving the goalpost with this comment a bit. My original comment says "may benefit from" being run under a "vanilla" kernel, as opposed to saying it would be completely non-functional under Android's kernel.
Presumably because container breakouts are fairly common and "external Linux software downloaded by the user" is at least as presumptively malicious as an app from the store. Modern consumer systems need to be safe vs. the user being tricked to run terrible things. A docker or whatever isn't quite up to the standards[1] required on its own.
[1] Though I'm very much not one of the pedants who refuse to see any security value at all in container isolation. Containers isolate software access (e.g. limiting access to libraries with vulnerabilities) and network communication (writing firewall rules for a container is a lot easier than it is for an app) really well, for example. Use them! But not for this.