Wat? You run LXDE/Debian on 756
bytes? Impossible. Running LXDE or even XFCE4 on my tablet with Linux Deploy took about 786MBs of RAM, not 756 bytes. But even still, that's not enough to do much comfortably. Not to mention that for X to work, unless you are using a native framebuffer (Unlikely due to the state of mobile GPUs, unless you have a Tegra, PowerVR or Freedreno-supported GPU), you still have Android's overhead and the X Server above that (For argument's sake, we'll include the X server in that memory estimate above, but not Android [though technically we should, since in this case, Android is hosting the Linux environment in a container] despite the fact that the X server is running under Android and not the chroot)
But then you'll have apps like Firefox and Chrome which will allocate memory for their use, along with any background processes. One reason your Android chroot may be so small (not sure what you run in it so I can't entirely debunk you) is because you are ignoring background processes (because only certain services are needed, and init isn't used by default in a chroot) and because you aren't using the distribution's kernel.
Now if you're using linux deploy for servers, wait, no, none of those will fit in 756 bytes of RAM. Anyway, that's enough of that, now to actually answer your questions.
The 3DS has 1GB of RAM hence my above rant. The Linux kernel uses the ARM9 Kernel-mode to boot, so the firmware is unloaded for Linux to start (no SD access that way) and is actually answered in a previous topic here on these forums:
https://gbatemp.net/threads/q-decrypt9-or-similar-as-cia.399418/ (Since both Linux and Decrypt9 are Brahma payloads, this is relevant)
I cannot speak for what the sdcard's tree should look like or what the resource usage is for X on the 3DS since I haven't actually compiled this project with X, only messed with weston/wayland (which is better anyway, you want X, build a copy with XWayland built in and use that as your X Server, it's still lighter than Xorg itself)
As for GLX Gears, it's an OpenGL test application that simply shows a small window with gears moving and spinning around. To answer the person asking if it would work: possibly, the fact that Wayland starts suggests some form of GLX support exists (even if it's software rasterizing), you wouldn't be able to run glxgears without XWayland though since GLXGears/Insert Your X11 Application Here doesn't speak Wayland.
pcs3rd: I don't mean this post to sound as inflammatory as it reads, my apologies if it comes off that way, I'm trying to be informative but I tend to be slightly abrasive while doing so.