How can I make PDFs appear life-size when displayed at 100%?

xorg.conf doesn't even exist on new installs nowadays because of xrandr. Most drivers work fine with just xrandr and no xorg.conf (I think Nvidia is the exception). What you need is to have xrandr run at startup all the time. I documented on the Ubuntu Wiki how to make xrandr commands run as soon as the GUI starts. Just use the same xrandr command you already figured out.

For Unity users reading along, equivalent directions for lightdm are here: https://askubuntu.com/a/69501/1158

That's actually a very complicated question.

I can't tell you how to solve your problem, but I can tell you why it occurs. Monitors have different pixel densities. A 1x1cm square on one monitor can contain a different amount of pixels that the same square on a different monitor. See http://en.wikipedia.org/wiki/Pixel_density for more information on that.

Because of this, 100% zoom will give you differently sized documents on different monitors.

Given this context, this question is probably better phrased as "how can I change what 100% means in Evince?" I don't know the answer to that. Sorry. I do hope my answer helps somewhat, though.

You are obviously on the right track, since you found that changing the DPI settings worked when you ran the xrandr command.

It used to be easy to change the DPI setting in Gnome itself, but apparently, Gnome 3 made this difficult.

You can check out this answered question on AskUbuntu for info about how to go about it in Gnome 3:

How do I change the font DPI settings?

There's a good answer on this blog about Display Size, DPI, and Text Size… an interesting DIY. He even includes a script to do the configuration automatically on startup. You will need to tweak it for your configuration though.