I think the "one surface rule" is for when you wait the 20 minutes for it to skim set and then assemble. If you are assembling immediately, I don't think it matters, but be careful you don't apply too much (use half the recommended bead size on both surfaces). If you over-apply blobs of cured RTV can break off the assembly and clog oil passages. A continuous bead is all that's needed.
You're probably OK that way if you skim coated the parts and you didn't see too much excess squeeze out from the outside (visible) portion of the assembly, plus you were doing water passages, not oil-wetted ones.