This bug never got a followup, but I can name three circumstances I know of 
under which it still happens.

1. Almost guaranteed to not be the problem, but it should be documented 
somewhere: If you use an Atom-based "nettop" where the external display is the 
only one used, it might appear you have this problem at first, however 
reconfiguring console-setup doesn't fix the problem—or rather, it only fixes 
the top left corner of the screen. Observed with Lenovo IdeaCentre Q150. The 
solution here is to modify the grub configuration (in /etc/default/grub) to 
disable the LDVS port the chipset thinks has a 1024x768 display connected to 
it, because the chipset is dropping acid and there totally isn't. Using various 
tools you can determine that the system does think there is an LDVS display, 
but turning it off in X11 or anywhere else won't make it go away. Gotta be the 
kernel command line.

2. If you have plymouth installed and working, you'll get a nice and pretty 
startup, but your font setting won't happen. I'm thinking I might hook setupcon 
into starting a getty and see if that resolves it. Hack solution, but I'm not 
sure if that'll work or if it does maybe that it's as good as it gets.

3. If your framebuffer driver loads late, the console may be set up in the 
initrd before your larger fonts can be loaded. Make sure that your correct 
framebuffer driver is loaded early by adding it to /etc/modules by hand if 
necessary and then running update-initramfs -u -k al.

There have been other issues with console-setup and the systemd transition that 
have since been fixed, but I was looking to see if someone had proposed a more 
elegant solution to #2 than I'm considering and stumbled upon this bug being 
open from ages ago. That means anyone reporting a bug that their system seems 
to have small fonts on boot is going to be looking at this bug to see if it 
describes their problem. These are the things I've seen happen and how to fix 
them, since none of them are really a problem in console-setup directly.

Joseph

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