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As a bi-platform user of Adobe software, I know exactly why you'd want to interchange the positions of the left Alt and Ctrl keys.
Unfortunately, when you use post-driver software (that works by intercepting keyboard interrupts), you put yourself at the mercy of "rogue" programmers -- such as those apparently hired by the Adobe Illustrator engineering department -- who have their own peculiar ideas about how things like this should work.
My solution might sound radical (and it's not cheap), but it works: Buy a keyboard that enables remapping at the firmware level. An example would be the Avant keyboards -- the descendants of the Northgate OmniKey series -- that not only give you key remapping but also some rudimentary macro programming capabilities. They even come with extra keycaps and a keycap removal tool so that you can, for example, keep the labeling correct on your remapped Ctrl and Alt keys. They use Alps mechanical rather than membrane-type key switches, which is great for someone like me (who does a fair amount of writing and loved the original IBM keyboards)... but I do understand that is a matter of personal preference.
As an added bonus, your key remaps and macros travel with the keyboard. Plug it into another computer, and all of your customizations are right there, ready to go.
I'm sorry I don't have an easier answer for you.
Dear Harron et al,
Interesting you should mention Northgate Omnikey. I loved those keyboards too. When my old Northgate was about to be retired, I ordered several of the keyboards and still use them on my desktop/tower machines. However, the present installation is on my laptop, which is now my main office system. I suppose I could get a USB keyboard of the type you mention and stop using the built-in one, but that would be awkward. I guess I will just have to train myself to use CTRL and ALT on the right instead of the left. And I will make a bug report to Adobe on this matter.
All the best,