Many plants will sprout preflowers after a month or two of veg, if so you can sex before flowering.
If you end up with too many females, pick the best ones that you have space for. Just because you sprout it doesn't mean you have to finish it, and it's not uncommon in gardening to plant more than you need and thin out the worst looking ones.
The size of the root system is going to be determined by a large number of variables, none of which is whether they are in flower or not (though I suspect what you really mean is after a certain period of time...). It's not advised to sprout more than one seed per pot however because thinning and transplanting when the root systems are mixed is a pain and quite error prone (meaning you will likely damage them). Single plants can be transplanted with no stress for the experienced, and minimal stress for even the novice if you follow some simple steps you can find all over the web. Far as transplanting, I start in very small peat pots, transplant to 1gal then 2 gal nursery pots, then 5 gallon buckets which are drilled with 1/4" drain holes. With smaller plants I have found that watering is much easier to get right in smaller pots, and it allows me to maximize space.
As far as the roots go, it really is more proportional to the plant size than other factors (at least in my experience). You can raise and flower a plant in a 1 liter pot, or even a dixie cup (the shot glass competition showed that you can sorta do it, but there really is a minimum size you can expect out of a plant

), but compared to something in a 5 gallon, those smaller pots will have much smaller maximum plant sizes they will support. If you have space for 5 gallons, then they will grow to that space, and you will just find that the plant will slow down growth dramatically when they run out of space. After some time you will get a very good idea of how large you want stuff, and you can tailor your veg time to growing plants to your flowering space. If you can't seem to get the plants big enough, then pot size is one of the first things you'd check.