When I was a young man, a pair of college students--John Tweet and Mark Hagen--published a tabletop historical fantasy role-playing game by the name of Ars Magica. The concept was that you played medieval European magicians, their companions, and their servants but the world conformed to the popular beliefs and metaphysical paradigm of the time. So no, things did NOT work as they really did- only as believed.
While that's interesting in itself, what I want to draw your attention to is how gameplay is meant to be organized: every player has a Magician (Magus) character, a Companion character, and contributed to a common pool of Servant (Grogs) characters. The Magicians were the lords of the manor, known as a Covenant, and each adventure had the players taking turns playing their Magicians, Companions, or one or more of the Servants. The reason? Because different sorts of adventures require different sorts of individuals to deal with them properly, and dealing with them can and does take time so you can't do everything with one character. (In addition, research is a big deal and healing often requires downtime.) In order advance the Covenant, players will need to shift roles (via shifting which character they play and when) to best meet the challenges put to them and their Covenant.
Groups of magicians are not the only ones that benefit from this perspective. So do (para)military organizations, the archetype being mercenary and trading companies. Noble houses, for all you Game of Thrones and Pendragon, also fall into this paradigm. Since I've been thinking in terms of giant robots lately, let's do in those terms.
A BattleMech mercenary unit (for BattleTech and MechWarrior) has more than 'Mech pilots in it. You have technicians, medical personnel, staff personnel, security/auxillary personnel, etc. and they collaborate to fulfill different necessary functions required to keep the mercenary company operational and viable as an entity- the unit itself is a player-character. A meta-character, if you will.
So why not do much the same thing? Have each player make a MechWarrior, a key auxiliary, and contribute to a pool of henchmen or minions. While not a direct translation of how Ars Magica's Covenants work, you can see the parallels and apply them in the obvious manner. The unit is the real character here, one shared by the players, and thus deserves its own character progression and development emphasis; this makes the loss of any given individual player's characters a little easier to bear.
You can use this for Macross and Gundam campaigns just as easily, since your pilots are going to be focused on their duties (and need to be combat-ready). I need not go on with specific examples; the point is clear- by embracing the organization as a shared meta-character, much as the Estate is in Darkest Dungeon, and allowing players to source individual PCs from it accordingly, you can maintain suspension of disbelief while allowing players to engage in a wider array of playable scenarios.
And yes, you the GM can do this too. It's how I get the players in my homebrew D&D campaign invested while rolling and running multiple characters- by letting each one contribute to the progression and development of the colony in concrete ways.