Cross-plane optical links would have a trickier tracking problem.
While there's no explicit mention of same-plane vs cross-plane optical links, I assume that the first time people have a public cross-plane optical link, they will make a big deal out of it. :)
The article also mentions that SpaceX would need to do further study before using laser links between satellites and ground stations-- this kind of optical link would require both more angular tracking and probably atmospheric correction as well.
I'm assuming two things: That something like Manchester coding is being used so that some clock skew is tolerable, and that the laser carrier is not in fact being frequency or phase modulated. Last I checked FM and PM of optical frequencies was not yet practical outside of laboratories, but I'm happy to be corrected.