Why? Because writing and signing a contract is expensive, for both the contractor and the government. So contracts are typically written in a way to make them very easy to extend, and existing contracts are often used as vehicles to tack on additional funding for new contracts. The original contracting agency would also usually charge a fee to the other agencies for use of their contract in this way.
So, this kind of glance at individual awards under a single contract is really too simple a view. A lot of these funds could be (and from my guess, probably are) going to completely independent projects from the randomizer.
TL;DR: Having multiple awards under a single contract is typically a sign of the government working around bureaucracy and attempting to save costs.
TSA later reported that the actual cost of the randomizer was around $47k. The total figure I had mentioned earlier was part of a larger contract with IBM. I saw the generic "IGF::CT::IGF MOBILE APPLICATION DEVELOPMENT" note on the award and assumed it was all for the same project.
It's also weird that TSA's response to OP's FOIA request cited a different and higher figure (~$340k) for the randomizer app -- I'm guessing they were grouping in other projects under the same award here too?
Besides, $47k seems like a reasonable amount if that figure includes training and deployment costs.
TSA spends most of it's budget through a provision called "Other Transaction Authority" which is essentially a vehicle to make purchases with barely any oversight from congress. http://time.com/4134368/tsa-price-of-security/ (Paywall)