How to map Ctrl + Delete to Fn + Opt + Delete with Karabiner-Elements
Fn  is usually evaluated within the keyboard, before transmission. It doesn't generate its own event.

According to Key Codes,  Fn   Opt ⌥   Backspace ⌫  generates this data...

Key Down
    Characters: 
    Unicode:        63272 / 0xf728
    Keys:       ⌥⌦
    Key Code:   117 / 0x75
    Modifiers:  8913216 / 0x880140 ⓘ


Maybe you could use that to initiate the replacement - I don't use Karabiner so can't test.

*Characters:  doesn't actually generate any printable character on my machine.