Here is what I did, and it appears to have worked.
Using plasmashop edit the dev_mode.dat like Chacal said.
You will see (custom) as one of the options of resolution. Type in the resolution you would like as well as 16 or 32BPP. SAVE
Then in your desktop shortcut type in "-iinit To_Dni" without the quotes.
ex.
"C:\Program Files\Ubi Soft\Cyan Worlds\Myst Uru Complete Chronicles\Uru.exe" -iinit To_Dni
What this does is bypasses URUsetup since it will try to override the changes you just made to the custom resolution.
(and since URUsetup was bypassed, you will want to make sure you already have a character in progress!)
Run and hopefully enjoy

It is pitch black, you are likely to be eaten by a grue.