Do you miss the function row?
And Alt + F4 is bound to a double tap of the right red thumb key :D
They (PyCharm, PHPStorm, etc) use a load of multi-key shortcuts which include use of the function keys and it became a real pig to use and ultimately I gave up (expensive - I'd bought 2; one for home, one for work...).
How do others manage this? Have another layer with all the usual keys but replace numbers with function keys? I don't fancy remapping all the shortcuts.
I just don't use F keys, but for number I have a left thumb key that transform the right side into a num pad. You could do the same with functions keys. Or do what I did for any number and permanently remap the normal number positions to f keys as you said.
But the nice part is you get to adapt the keyboard to your own needs. If you only use one or two function keys, you could give them decicated buttons on the may layer. You can even have one button do the whole combo. For example I have one that does shift+insert so I can more easily copy into terminals.