It depends on the strain, but when 12/12 from seed there is not the time for the plant to grow very large. There is a very comprehensive thread called something like 12/12 from seed, here we go
https://www.rollitup.org/indoor-growing/416589-12-12-seed-thread.html
del has gotten upto 8 ounce a plant going 12.12 from seed. With regard to flowering time, i am very surprised to be reading about 6 week flowering autos, most i have looked at in the past have all been 8-9 weeks. The flowering time of a photoperiod (ifi ever state reg in context with auto's i simply mean photoperiod and not regular sexed seeds as opposed to feminized) when grown 12/12 from seed will not be that much longer than the strains flowering time, but as i say, the range of genetics is absolutely huge in comparisson to the available auto's. Outdoors auto's have their use, but indoors, it just does not make any sense to go auto's especially if you're paying for electricity (even with cfl's, every little helps

)
As to pot size, i have only ever used a sigle sized container when doing a soil or coco grow so cannot comment if that keeps them small, but going on some of the photo's i've seen of monsters growing in pots half the size of mine, i do not beleive that it is a factor to bear in mind.
With regards to regs versus fems, there have been quite a few comprisson grows done and more often than not the plant from the regular seed far outperformed the plant from the feminized seed. All depends on your needs, but i personally like to plant seeds ahead of time and find myself a vibrant female to keep as a mother plant for a few grows. But if you're not able to do this then yes, fems an be great, nothing worse than having to cut your potential harvest in half due to a handful of males i your cupboard.