I had an MX, the finder was useless to me - felt like my eyes were going to roll out of my head trying to check the corners. The EOS 3 may by .72X on paper but it's still super bright and clear and just "feels roomy." My EOS Rebels are all ~.72X as well but definitely feel dim and confined by comparison.
Correct, more magnification means less eye relief and less magnification means more eye relief. Fortunately with AF, you won't depend on the viewfinder to achieve critical focus whereas on a manual camera you do.
Of course with tiny viewfinders, you can use magnifiers to attain huge magnifications of the center area for much better manual focusing.
With manual focus cameras you are stuck with the viewfinder as well as the focusing screen if they are not interchangeable. As above, you can also use magnifiers.
However, cameras with interchangeable viewfinders and focusing screens - such as the Pentax LX, you may get to choose both. Additionally, you have a choice of perspective with the addition of the waist level.
With the FE-1 you get the massive 1.35X magnification, 1.0 with the FB-1 + FD-1, 0.9X with FA-1, FA-2, FF-1, 0.84X with the FB-1 + FD-2 and the most eye relief with the FB-1 + FC-1 sportsfinder. The FA-1, FA-2 and FE-1 also have diopter adjustments.
BTW, unlike other aperture priority interchangeable VF cameras, you can actually use the LX without a viewfinder - cheap waist level option, because the full info are visible and the meter is not influenced by external light.