To my knowledge that low branch is more likely to be a sucker that will take strength from the top of the tree - unless you're looking for a multi-trunk design, my understanding is that it is best to remove those. Just FYI. Pomegranate suckers easily - I'm finding some on a regular basis that need to be removed on mine!
In terms of pot size, don't you want to only double or triple the size of the pot? I was wondering about this myself - if you throw a seedling in an Anderson flat it's going to be pumping energy into growing the roots rather than growth for development, or something along those lines, no? I was kind of thinking of taking some seedlings and putting them on boards in flats, but now I'm re-thinking it. Just thought I'd bring it up as something to consider.