There were a couple of options for doing this in a way that may not have required a chroot, but the bigger issue then is: how do you install Ruby? or Python? or [whatever]?
I'd think it fairly necessary to have a full Linux environment (and ideally good package support) underneath the IDE in order to actually work with the editor. And it works quite well in practice due to the integrated terminal that's running full Ubuntu (as you've said, due to the chroot).
The comment is fair, but I've tried to explain this as clearly as I can in both the website and the installation script itself (there's a confirmation explaining exactly what will be done and what that means, although I obviously try to keep it as straightforward as I can without obscuring anything - at least not intentionally).
The native part refers to the architecture. It executes natively on ARM, rather than through some kind of emulation solution (like QEMU) that would make it untenable in practice (I've been dogfooding the scripts with this for some time while trying to polish the process).
The instructions also mention that you can just install into an existing chroot as a standard apt-get install call for anyone that has one set up already and knows what they're doing, although it should also work side-by-side.
I'll review the website in light of your comments though, to see if there's anywhere this can be made clearer!