But wouldn't upgrading to a larger colonization vessel cost enough money to push it up to 100BC?
The point is not so much the cost, as clanlindsey has implied, but the time they take to build. Both values are quantified in BC, so it's easy to confuse them. You are correct that it does cost you more money overall, but the entire point is to get colony ships out as fast as humanly possible.
When you upgrade a bare hull into a colony ship, it gets 1M colonists placed on it, so you can get away with not returning it to a planet to refill it first. Since DA introduced "spored" growth, where a planet below the 75M base growth has anywhere from 1-5M pop added to its growth, before bonuses, this isn't as detrimental of a strategy as it probably should be. The growth and the base are low enough that stacking growth bonuses on almost doesn't matter-this strategy relies on ferries more than it does on real growth-but Breeder would still help enough that the colonies could support themselves in a relatively short period of time.
True, a default colony ship has a hyperdrive, granting it 1 more speed than base (which in TA is 2). Thanks to TA's base 2 speed, and with impulse drive researched, our speed is 3 for a bare hull, or 4 for a colony ship. The colony ship will get there faster, but it doesn't matter if it takes us twice or even four times as long to build it. And the effect is magnified the more speed bonuses you tack on-for instance if you're playing as Terrans or with their tree; the innovation complex is horrendously valuable in that respect.
Taking an economic bonus won't help you during the colony rush, because you're spending more money than you could possibly make, your populations are ridiculously small, and your tax rate is ideally too low to make any money of significance to stimulate growth.
There is an exception to this if you take all economic bonuses with the DA Thalans, as they will then break even at about a 29% tax rate (if memory serves) on new 250M pop colonies, but that's about it.