Not...really. unlike conquest, the clans are not inherantly opposed to working alongside each other. In conquest, all the factions are seeking just about all others' destruction with the Space marines and IG working together. The wheel was forced for sake of what made more sense in an otherwise non compatible set of factions.
Even Spider has allies in other Clans (less so in Scorpion and Crab)
Alliance and Oath of Fealty were more synergy cards for people splashing personality to obtain rare ebenfits that were clan exclusive.
Some of the 40k thing with allies is depend on the factions themselves. Lore wise, the Eldar could work with Space Marines, IG, or Inquisitors depending on what's going on. This is to a lesser extent with other factions (i.e. the Tyranids just want to eat everyone or that Khorne hates Tzeentch).
With L5R, whoever can "ally" with who was based on the story at the time. That's why we see someone like Kitsuki Akito or Kitsu Asato . These tend to be exceptions though and having some clans go better with other clans could work with both story and game situations. Putting story reasons above game reasons is preferable to me because of the whole story prize situation that the game has. I'd much rather have players have a large say, but not the only say, in which clans they can be allied with.