In-universe, the Prime might find use as courier. It is fast and stealthy, quite good fit for transporting important stuff that can't be entrusted to lesser things (and assuming air transporting is not possible for whatever reason).
In real life, i assume it is to keep the design pure. As it is, the intend is to use the UAC/2 and ATM-3 ER missiles for long range plinking. CASE II is used, heat is not an issue, light active probe doesn't work with stealth, light TAG doesn't fit its mission profile, an ER small laser would mar its simplicity, so what else to do but add cargo space?