So, here's my idea. I am really into Warcry right now, and have been houseruling a few models in, with some success. I don't play Seraphon, but their Mesoamerican theme intrigues me, and i've always liked the idea of Lustria. So, I thought i'd create an account here - I usually lurk about in the Grand Alliance Community as AthelLoren - to ask all of you Seraphon experts over here if you would support House Rules for them. Just post to give ideas of which troops you would like to see, how they would fit lorewise, etc. I ask this because I was considering using the Warcry rules for a campaign based in a sub-realm, halfway between the realms of Life and Death, called New Lustria, and it seemed appropriate to have Lizardman survivors from the World that Was hidden away inside, or at least some Seraphon coming to repopulate it.
My main problem with WarCry in general lore wise is that I see no good reason why Seraphon would join those skirmishes in Abaddons domain. But your idea of using the rules for making a story campaign is intriguing. I use the regular AoS skirmish rules for smaller missions of the story campaign that I am running for my friend, that they are kinda lackluster in some ways. Sadly I don't know know the warcry rules well enough to make suggestions. Lore-wise you can do almost everything with Seraphon, as the AoS lore doesn't define clearly what and where Seraphon are and what they do, or don't do.
To be honest though, GW made pretty pathetic lore excuses for some of the factions that are playable in Warcry. Daughters of Khaine certainly shouldn't be there - they have no means of teleportation or anything that would allow them to get into Archaon's realm's unscathed, and if a load of half-naked Witch Elf tarts could fight their way into the Allpoints, pretty much anything else could. Seraphon could teleport in, Fyreslayers are obviously superior to Witch-Elves anyway so they would be able to fight their way through, Kharadron could blast their way through in their airships and airdrop their troops... the list goes on. I say go for it - I thoroughly support the idea of developing house rules in situations like this where GW have made such rubbish decisions that just don't fit, and certainly endorse breaking their canon if it means bringing something that fits better than GW's actual decisions to the table.
Lore wise the Slaan could have teleported a small force to deal with a member(s) of a warband they have foreseen gaining influence and becoming a problem in the future. They see it fit to send in a hand picked team of Seraphon to achieve this goal rather than unnecessarily committing to a full scale invasion of he chaos realm.