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