Yup. One of the hallmarks of CTers is that the conspiracy has to get weirder and weirder as the first bits are debunked. Ed forbid that the theory should fall; no, the detailers just get more complex.
So someone comes up with "controlled demolition." Well, as you point out, one of the things done in a controlled demolition of a steel structure is that the structure is weakened -- some columns are cut entirely, others are cut part way through, etc. An operation which takes months and couldn't be done without being noticed by the actual people in the buldings, who presumably would object to someone stripping off the sheetrock and cutting slices into the columns which are holding them up. So now someone has to come up with a way for the building to undergo "controlled demolition" using methods other than those traditionally used for "controlled demolition." Aha! Thermite is very hot when it reacts! It could 'melt' the steel! And because it's 'less' controlled than an
actual "controlled demolition," that explains why the towers didn't fall in their own footprints like they had earlier claimed.
Because that's not what is usually done with thermite and because the steel did in fact heat far enough to weaken, it becomes difficult to debunk. Or in other words, it's difficult to debunk precisely because it's so ridiculous.
The Loosers are reading this -- just wait. Because you correctly mentioned that a thermite reaction takes some time to get underway, they'll probably incorporate that to 'explain' why the towers did not fall at "free fall" speeds like they've been claiming.
ETA: In fact, they'll probably cite the new "fact" to a "military demolitions expert with experience in the steel industry." So congratulations! You could have your words twisted beyond recognition by a CTer.