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Unfortunately, the Photoshop way also exemplifies a problem with assigning (almost) every action with a shortcut - with so many you inevitably end up clashing with something that either means something else in another app or is already taken by the OS. Another issue is that some shortcuts that make sense on a US keyboard are completely non-sensical on a foreign language or UK English keyboard because the keys either don't exist or they are located in totally different places.

Once you get to grips with adding shortcuts using system preferences (and btw, I try to use the three key "command-alt-ctrl" chord as it definitely doesn't clash with anything else, yet it is still incredibly easy to press), I think you end up preferring it. Not only do the shortcuts make sense to you (so they are easier to remember) whereas in-app ones very often don't once you get beyond the most common commands, it also makes it a lot easier to apply them to the same actions in all other apps when they exist. However, the major downside is when you move to another persons Mac and they don't have any set up!