You use Thunder III for Thundercloud procs and Thunder II when refreshing manually during the Umbral phases.
Though the tooltip gives the impression that the Thundercloud potency is determined by the dot it procced off of, this is incorrect. If you get a Thundercloud proc off Thunder II, you can use Thunder III for the proc and get full benefit of Thunder III (potency and extended durations).
This is also one of the few cases where you may have to alter your rotation as a Thunder III proc will extend for another 24 seconds. In this case, you may be better off using Scathe after Blizzard III if you think your Thunder is extended long enough to last another Fire cycle.
Optimal rotations are based on ideal circumstances, this is true. However, it's good to know how to use your class at full power and then adapt it from there.
It's also especially easy for a BLM to follow the optimal rotation since even if there's a lot of movement, you don't have many timers to monitor. In most cases, you should get roughly the same amount of Fire Is each astral phase and regen with Blizzard III --> Thunder II --> Fire III. When you move, you can usually just pick up where you left off.
It's only a pain if you lose the Astral Umbral buff completely, but I don't think this happens that often since it's very forgiving.
Fire III is not good dps because it kills your mana and it's gains in crit do not make up for it. It's not a mana efficient spell and you can only get like 3 off each Astral phase and you will never get a Firestarter proc spamming so you're not taking advantage of that trait. I'm sure PessiMistic or another better mage can show you the math that proves that Fire III spam is never optimal even with crit gains.
Though I have heard something like Flare spam working with two targets, but I've never tried it myself.
I like PuroStrider's spreadsheet which gives good comparisons on the different spells and answers some of these questions that you may have.
Here's a link to the spreadsheet and the thread.
Synovius's thread on the rotation is also helpful if you want some tips as well. Another link
The most important thing about understanding optimal rotations is not to follow them blindly but to understand how abilities rank and work together with one another. Feel free to adapt them depending on the situation but to do that, it's very helpful to understand what the ideal spell rotation is and then change it from there.



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