In theory, you're loosing on some, possibly minor, stuff.
1) If you're main character is an origin one, there are some lines in dialogues you couldn't choose otherwise (i.e. as Ifan you can entirely avoid some confrontations, which wouldn't be possible otherwise).
2) Some solutions/options for origin character's quests are available only if you play as those characters, and you are able to unlock related achievements only when playing as them...............
What if I have these origin characters in my party with my custom main? Can't I just use the origin characters to interact with NPCs to achieve those origin tagged solutions/options?
For example, If my main is custom character and I have Ifan in my party, can't I just use Ifan to interact and use his dialogue lines to avoid the confrontation that you mentioned in point 1?
Nope, the companions decide for themselves, even most of the time you cannot intervene or even hear what are they talking with the NPC. You can only make decisions on the Origin stories if you are that character, If not you can only help (or not) them and only have access to full dialogue if you are Ifan, Sebille, etc.
You also lose one character quest (you only have three origin quests instead of ffour).
Also there are lots of dialogues with your companions that only happen when you are an origin character and make a breaktrough in the story and talk with them.
In the event that your companions have quest or story related dialogue with another NPC you are interacting with; the companion will pipe up and ask to talk to them. This dialogue is slightly changed if it was initiated by the origin character themselves, but ultimately conveys the same information.
I think you need to stop worrying so much about the specifics, you will get the same experience.
I did not finish the game with all characters, but if you are playing Sebille and Ifan you can make some decisions that can potentialy change a lot in comparison with the Sebille and Ifan companions ( people you decide to kill or not, places you do not go, and something with Ifan in Arx, for example)
