MacOS – Custom keyboard shortcuts/mapping

I have been fiddling around with the keyboard shortcuts in sys preferences, and have to say the options seem limitless, and fantastic. I'm a huge keyboard user and will do everything I can without using a pointing device.

I have however a huge preference for using the bottom-left-most button for all modifier actions (instead of the default Cmd ⌘ ). This is not even related to "being used to how Windows works", I simply find it very uncomfortable to use Cmd ⌘ – the Fn button on my laptop is actually what I've been using.

So – I could not find any other way than to use the custom shortcuts, and had to map each action one by one. I set most of them to "All Applications" (Copy, Paste, Cut, Save, Select All, Undo, Redo, Refresh, Close Tab, etc.)

My issue is this : because we have to use the exact Menu Name, it turns out that setting Ctrl ⌃ W to "Close Tab" in Google Chrome, will not "Close tab" in Filezilla.

It also turns out that I cannot re-use Ctrl ⌃ W for more than one action. In other words, I can't use custom shortcuts if the action has a different name in different software.

Is there a way around this?
Much appreciated,