The short version: in function rgb_matrix_indicators_kb() in file keymap.c, use function rgb_matrix_set_color(). For example, to set a blue colour on key F7 on a Keychron V5:
rgb_matrix_set_color(7, 31, 13, 200);
That is for a V series Keychron keyboard (and presumably for all keyboards in the main QMK repository that are physically capable of it), but it is more complicated for later Keychron models, e.g., the K Pro series, where rgb_matrix_indicators_user() is hijacked in common/wireless/indicator.c in function led_matrix_indicators_bt().
Introduction
It isn’t well advertised in the QMK documentation or any examples you may find elsewhere (there is too much emphasis on animations, which are really only for demos and are completely useless for any real work), but it is entirely possible to set the colour individually for each key, not just the same colour for all keys (if the keyboard is physically capable of doing it and the hardware for doing so is supported in QMK). And for the commercial QMK keyboards and for the boards where the animations already work, everything has already been set up.
Confusing QMK terminology
RGB lighting: This has nothing to do with the LEDs on each individual key… The magic word for that is “matrix” and the combination “RGB matrix”. “RGB lighting” and “RGB matrix” are two completely different things. And there are two more: “LED matrix lighting” and back lighting (the latter using PWM capable I/O pins on the microcontroller to control the brightness)
Unnecessary or even detrimental: BACKLIGHT_ENABLE and RGBLIGHT_ENABLE
As for compile-time configuration, only RGB_MATRIX_ENABLE is required and it is already set up if the RGB animations work. Thus it isn’t required to change any compile-time setting if RGB animations work. For instance, that is the case for the default Keychron V5 QMK part.
For instance, for Keychron V5, the (hardware) definitions are already set up in qmk_firmware/keyboards/keychron/v5/iso_encoder/iso_encoder.c. And it is also enabled by default in rules.mk:
RGB_MATRIX_ENABLE = yes
Note that BACKLIGHT_ENABLE and RGBLIGHT_ENABLE should stay as they are for this purpose (= no):
BACKLIGHT_ENABLE = no # Enable keyboard backlight functionality RGBLIGHT_ENABLE = no # Enable keyboard RGB underglow
Despite similar sounding “RGB”, “light”, and “backlight” they have nothing to do with setting RGB colour for individual keys; the LEDs in that case are some other LEDs, separated from the individual LEDs for keys/switches. The confusion comes from the weird QMK lingo.