In battles there are five party spots (including Ramza), two guest/enemy spots, nine enemy exclusive spots, for sixteen spots total.
The guests are technically NOT taking up spots, there's an early mission where you have 4 party members including Ramza plus two guests (Algus and Delita), the game is just limiting your party's size in story missions. I'm pretty sure there is at least one mission each where you're limited to every possible variation of party size.
For missions where there are guests it's just the game's tendency is to limit your party lower than 5.
It sounds like you're less worried about winning and more about irrational levels of symmetry, which is understandable, but I think you should reconsider because of what else the game has to offer. Unless you're obsessive enough to count which characters are attacking to make sure everyone is getting the exact same XP and JP allotments, you're going to have asymmetry no matter what, and I assure you that you will not be setting yourself up for failure. If you're worried about being underleveled you should save after each story battle, then start the next story battle to see what level the enemies are then load your game.
I would ask you to please try playing some more, but this time pretend that your max battle party size is 4 and the fifth character is just a bonus, or if you really want to waste some time you could upgrade your party to 6 or 8 and rotate people out so everyone fights the same number of battles, but again unless every character does the same number of actions they will never be making the exact same gains.
Before you begin to cope with having to choose which party members are going to be one level (!) behind the rest of the group, I would also point out that you can get unique permanent characters as well as breed monsters, which will further complicate your decisions.
Edit: Also, I'm curious, what other RPGs have you played and how have you dealt with this problem in those games?