I disassembled my mill into several components to get it into our townhome basement but checked out the mill thoroughly before doing so just to be sure that there were no issues before disassembly. I'd recommend the same for anyone in a similar position.
I had one or two very minor warranty issues that were handled satisfactorily by Tormach right at the time of the disassembly. There were a couple of other issues after the warranty period expired and those were handled just as professionally even if one of them did cost me a few bucks. I felt very fairly treated, however.
If you are seriously considering the extended warranty, I would check with Tormach and see what they say about that and a disassembled mill.
I suspect that the warranty disclaimer for disassembled mills is primarily there to limit their responsibility in the event that an owner completely hashes the job.