All Canon models except the 1dx which received additional tweaks are the same: for optimal iq use only full (analog) iso stops, everything else is digitally modified like iso1000 is iso1600 underexposed. Intermediary iso steps are only for jpeg, video and auto iso with fixed shutter/aperture.
Actually, ISO 1000 is 800 pushed, so is much better to use 1250, wich is 1600 pulled.
Anyway, in my experience too, Lower ISO = better IQ, I just avoid pushed ISO's (125-250-500-1000...).
In theory, even ISO 640 has less noise than ISO 100, being 800 ISO pulled, but as far as I'm concerned, images at 100 ISO are much better. Colors and nuances are cleaner and DR is wider.
If you use Magic Lantern, I suggest you to use ML ISO's, highlights rolloff is smoother and even shadow noise is reduced. The advantage is not always noticeable, but sometimes it is. What's more, you can use ISO 80, which can be useful in strong light situations.