I know that Rune tokens appear in home realms of players (all 3 of the areas). However, what about the areas outside? (Those 2+ areas)

I did not place any rune tokens on them throughout the game, but there were some cards that made references in such a way that it was 'common' for rune tokens to be found outside the home realms. This made me worry that I am playing wrongly. I then cross checked all the cards and found a few (very rarely so, mind you) cards that would cause rune tokens to be moved onto outside areas (e.g. one card called Threatened Home Realms or something)

The question:

Is it part of the game that there are VERY few rune tokens outside home realms? Or did I miss a step to randomly place a rune tokens on all outside areas at the setup portion of the game?

You don't start with any outside home realms. Some games, they come out quite frequently, but in other games, they can be sparse.

7 of the 8 Winter Season cards give the opportunity to place more Dragon Runes on the board. With 4 of those, at least one WILL be placed on the board, no matter what; for the other 3, they may or may not, depending on the situation (and whether the players opt to do it). (For some of these, a fake one will appear also)

Any time a player completes one of their Objectives, a new Dragon Rune will appear. (one real, one fake)

Any time a player turns in a Timmoran Shard reward card, a new Dragon Rune will appear. (one real, one fake).

The Favor of Kellos Tactics card will cause one real and two fake runes to appear.

If a player has the Captain of the Heroes League card, any time that player discards 3 Rewars, a new Dragon Rune will appear (one real, one fake).

Thus, during the course of the game, more runes will appear. It depends on how the cards play out on how frequently they come into play, but they always will come somehow.