Soul Secrets are actually a little bit too strong at the moment because their level 15 feature is overpowered and needs a little nerf, but I didn't have time to change it.
Applying extra runes means being able to get to a legendary weapon faster and to break the bounded accuracy that is so important in 5th edition, so absolutely not.
Having 2 runic items is something that was allowed to all runeseekers previously but that I decided to change exactly to avoid having soul runeseekers with two talking NPCs, which is very annoying to keep. Either the DM or the player need to account for the existance of a talking NPC the whole time and it's more work than it seems, especially when there's two attached to one player.
If you really want to buff them just enhance the current features, use a larger AoE for example. But I wouldn't do that, it's already dangerously strong.