> almost all terminals cannot differentiate between Enter and Ctrl+Enter

On the contrary, many (perhaps even most) of them can. This is a matter of having a keyboard map that makes these into two distinguishable actions. For many terminal (emulators, at least) this is indeed entirely within the remit of the keyboard map and not limited by the terminal emulator itself at all.

Easy to find example: The us.kbd keyboard map on FreeBSD, used by the terminal emulator that is built in to the kernel and that provides the kernel virtual terminals, distinguishes between these two chords, mapping the former to CR and the latter to LF.

    /usr/share/vt/keymaps % sed -n -e '3,5p;/089/p' us.kbd
    # scan                       cntrl          alt    alt   cntrl lock
    # code  base   shift  cntrl  shift  alt    shift  cntrl  shift state
    # ------------------------------------------------------------------
      089   cr     cr     nl     nl     cr     cr     nl     nl      O
    /usr/share/vt/keymaps %

Note that to take advantage of a mapping like this, one has to turn off the crnl input mode in the terminal line discipline. Again, though, the kernel line discipline is a separate thing to the terminal emulator and this is not a mechanism of the terminal emulator.