I agree with much of what you say (though I really think you're not giving enough credit to Manawall and Manaward, especially in your T13 example - it's godly to singlehandedly negate a final phase Earthshaker set by popping Manawall after the first hit and then Manaward and let your healer do whatever - free set of DoTs on the boss!!!) but I think you're glossing over what happens in FCoB realistically (perhaps your points are targeted more for future content, though with the level increase it will all be moot to consider current tools). Having STR Virus just means SCH Viruses the boss when it's time, that's more or less all there is to it and literally the only difference in having SMN's Supervirus is SMN can apply it himself because the SCH is lazy, and a slightly higher upkeep of E4E isn't enough to change much of anything. Beyond that, BLM mitigation trumps anything SMN can do currently, because it can mean survival of both you and others, or at least give more healer DPS, especially when things get put on farm (but in progression Apoc was amazing during mess-ups, preventing death and clearing > rezing dead person IMO). Even in progression, if someone died, a healer picked him up, and if there were so many deaths that neither healer had Swiftcast and someone was still dead, it was a wipe.
Honestly, if I had to choose to have BLM tools or SMN tools (not related to how they attack, just their tools), I'd choose BLM tools as of current content.
What I'd like their difference to be, DPS wise, and this is assuming resources aren't an issue, BLM would be 90%-110% depending on mechanics and procs/crits, where 90% is an average run and getting caught in mechanics, and 100% is a good run + mechanics or an average run + no mechanics, 110% is a great run. SMN should be a solid 95-105%, 95 being mechanics + normal run, 100 either mechanics and good crit Festers or no mechanics and a normal run, and 105% being no mechanics + good crit %, tuned very close to what the average BLM damage will be. I do think they should average out near the same damage if you repeat a fight multiple times. Give SMN a resource fix and the equivalent of 20 extra ST DPS (i126 SMN with i135 book, I've tested this ... a lot ... and the results would make you cry ... crafted i110 BLM can do about the same DPS on average) and they're in a spot where SMN or BLM could come to raid and no one would groan either way.
Even assuming full resources, SMN would lose to everyone but BRD and pre-2.45 DRG in T8. With resources it was BRD level, and that's assuming a BRD who sings Paeon's a portion of it.