Thundercloud is a 5% chance, so it's not really instant in every instance, also you have to actually initially cast Thunder III in order to receive a Thundercloud proc. I start my single target rotation with Blizzard III, then immediately use my swiftcasted Thunder III macro for the instant thunder, then start into my Fire III. When I cast Fire III it's super fast, because I'm already in Umbral Ice III and my MP bar is also completely full. I don't think my Swfitcast would ever be wasted on a Flare, because I only use Flare in AoE situations and I also never use Thunder III in AoE situations, so it works out as being separate without the interference.