Agreeing that it would be nice if the two sets of configurations were integrated together, there are two reasons why they are different:
- they evolved separately (and no one has proposed an integrated solution which satisfies the requirements of both), and
- they have different requirements.
The Linux virtual consoles provide a terminal interface which supports POSIX termios: what you might consider low-level character I/O. That was well-defined by the mid-1980s, with technology from the preceding 10 years. The termios interface is concerned with control characters, a few video highlighting features for a single small font, etc. It does not make a lot of assumptions about the keyboard other than that it can send characters.
X11 came near the end of the 1980s, designed to support graphical I/O. It makes different assumptions than termios, e.g., graphics implies multiple fonts (and the ability to display a wide range of characters). Also (because of the need to handle a mouse or other pointer device), it needs additional methods for handling input.
Unlike the termios interface (using a sequence of characters/bytes), X11 passes information by events which hold a lot of information, and events can be combined in ways not contemplated when termios was devised. Thus, rather than encoding control and shift into a character, an X11 event might pass the control modifier as one event, and a key code as another event. The X11 libraries combine those events.
Though both were existing technology from the outset, X11 (even as X386) was less widely used, and basically came too late by several years to influence the design of termios. That was all done before Linux started. Since there was (and apparently still is) no alternative design which provides a distinct advantage, there's been no change since the mid/late-1990s.