Solution

The title and colors in the puzzle clue Symbolic Coordinates. The letters are the first letter of each symbol in the module. (The names are disambiguated by the tutorial video).

Letter	Symbol	Name
F		Flag
P		Pluto
C		Coffee Stain
T		Tunnel
V		Vortex

The letters translate into another letter while the colors provide a number.

Given letters	New Letter	Given Colors	New Number	Given Letters	New Letter
F T V	M	Y G P	6	T P F	D
F C P	S	P G A	9	V C F	L
T F V	P	G A P	7	P T V	U
F C V	W	Y A P	3	P T V	U
C F P	N	P A G	5	V F C	R
P C F	V	A P Y	8	T P F	D
F V T	G	G P Y	2	V C F	L

Here, the flavor text becomes important. It clues at using Friendship and the edges of the Friendship table.

The first clued letter shows which letter in the Friendship table to use. The second clued letter shows what edge of the table this letter should be found on (U = Up, D = Down, L = Left, R = Right). The number is an index into the name of the pony that is next to the letter.

ScrewBall

ThunderlAne

Cheese Sandwich

ChEerilee

LighTning Dust

Ms. HarshWhinny

TOe Tapper

This spells the clue phrase BASE TWO, which is another way of saying

BINARY