My first post - I can't resist clarifying a few things...
X-Amiga is a custom Linux, built from scratch - not a repackaged or cut-down distro. I mention Gentoo in the 'About' page because that's what I used to build it! However, apart from the kernel, nothing else is inherited from that distribution.
It's as 'un-bloated' as possible. ~40MB may seem excessive, but half of that is taken up by the kernel, some by the splash graphics and the rest by mostly essential packages. It has networking, CPU frequency adjustment, USB access, security... Not too bad. I still intend to cut it down further!
A large kernel has no impact on speed. Very few services are started up, and the kernel itself is optimised for running one program well (E-UAE).
The one screenshot I've posted on the site is of the installer. It's just Linux, on a bootable CD. The window manager is called AmiWM - it mimics the look and feel of the Amiga. There's also an OS1.x mouse pointer theme. The shell is just a customised ATerm, and the familiar-looking file manager is Worker, a DOpus clone. No emulation is used here, it's all just Linux.
The installer (a GTK dialog script) copies a suite of packages to the destination, together with the kernel and some scripts. And E-UAE, of course. Again, this part is all Linux. The only Amiga files to be copied are your legally-acquired ROM(s), and a pre-installed operating system (whichever one you want to use: from 1.x to 3.x).
It won't overwrite any existing data partitions unless you tell it to! I was extremely careful about this. The summary screen warns which partitions will be deleted; the user has an opportunity to change the destination or abort installation, and only at the end - when pressing the 'Install' button - do the changes become irrevocable.
I suppose X-Amiga could be considered a Linux distro in its own right. In any case, all the installed packages exist only as infrastructure for E-UAE. And while E-UAE might not be as far along as WinUAE, it runs on an Open Source operating system: Linux. That's good enough.
The main reason in creating this was to provide as seamless an 'Amiga experience' as possible. So there's no scrolling text, no configuration screens, no icons to click-to-start. It boots as rapidly as it can into a genuine Amiga workbench. When you exit, it shuts down the computer.
I know Amithlon is better. I can claim only that X-Amiga is also a good solution. Naturally, I'd welcome technical input from users. I'm documenting everything; it's all wide open to peruse and hack!
Anyway, I'd better get back to updating it... Sorry about the boot problems!