The Potential Rule
I have actually done some more research and I think I found the answer in an unlikely place, Unearthed Arcana. It is Unearthed Arcana, so take it for what it is, but it has this passage in a sidebar:
Multiclassing And Variant Classes
Multiclassing between variants of the same class is a tricky subject. In cases where a single class offers a variety of paths (such as the totem barbarian or the monk fighting styles), the easiest solution is simply to bar multiclassing between different versions of the same class (just as a character can't multiclass between different versions of specialist wizards). For variants that are wholly separate from the character class—such as the bardic sage or the urban ranger—multiclassing, even into multiple variants of the same class, is probably okay. Identical class features should stack if gained from multiple versions of the same class (except for spellcasting, which is always separate).
It does include the caveat "from multiple versions of the same class" . But I think this is a suggestion that class features should stack, except spellcasting. It is possible that the text included in many prestige classes regarding the stacking of sneak attack, turn undead and Uncanny Dodge, is the version of this rule that they eventually ended up with given UA's playtest/pseudo-house rule status.
While UA certainly is fraught with dubious rulings, we have no ruling of how class features stack/don't stack in the general sense. We have certain specific instances, but no general rule. UA provides the closest thing to a general rule, and hints at RAI, but it is itself a specific rule as pointed out in the comments.
Applying it to the question
Here are the two instances of Combine Song, first from Seeker of Songs and then from War Chanter
Combine Songs (Ex): A seeker of the song of 2nd level or higher can combine two types of bardic music or seeker music to provide the benefits of both. The seeker chooses two music abilities and activates both using the same standard action. If either or both require concentration, the seeker can maintain concentration on both by using one standard action each round to concentrate. The normal stacking rules for bonus types apply to music abilities combined with this ability.
Combine Songs (Su): A war chanter of 5th level or higher with 12 or more ranks in any Perform skill can combine two types of bardic music or war chanter music to provide the benefits of both (normal stacking rules for bonus types apply).
In putting these side by side I notice two things, that I think actually make them different abilities that, unfortunately, have the same name.
- Type of Ability: Seeker of Song's is an Extraordinary ability, where as War Chanter's is a Supernatural ability
- Ability requirements: Both require levels but only War Chanter requires ranks in perform.
If they are separate abilities, they definitely stack. If not...
I would say that given the absence of a RAW for whether class features outside of those that have specificstack, we have to make judgement call based on RAI which is ultimately up to the DM.
I think that it is clear that they do stack, given that every specific rule we have says that the specified abilities stack. Each adds one extra song in each instance for a total of three.
Restrictions
The RAW do lead to some interesting restrictions on what musics can be combined.
The following combinations are legal
- 3 Bardic Musics,
- 1 Seeker Song, 2 Bardic Musics
- 2 Seeker Songs
- 2 Warchanter Songs
- 1 Warchanter Song, 2 Bardic Musics
- 1 Warchanter Song, 1 Bardic Music, 1 Seeker Song
But these are not legal, due to the fact that both specify combining Bardic Music and their respective songs.
- 1 Seeker Song, 1 Warchanter Song
- 2 Seeker Songs, 1 Warchanter Song
- 2 Warchanter songs, 1 Seeker Song
- 3 Seeker Songs
- 3 Warchanter Songs