First and must importnat remember it protype means that warp five engine. NX Enterpise did not test the top speed until they had to. UFP want more testing time. Talk about give next generation of cargo ships warp five drive partly back this claim.
Secound only advance the warp five drive offer was speed it did not generation more power then warp 4 drive. This back fact that in thoery NX Enterpise could gone up to warp 6.5 by some minor changes to the warp drive itself. Only other piece of evindece that that Star Trek Twlight were at least one Reptilian ship had been destory off screen. Fact decide send two the ship attack Intrepid. That one Xindi starship destory on screen. Other last fact Xindi board party only 4 soldiers. If starfleet officer not injured the team get wipe out. Since fire broke out between three engineer crew members and took cover able hold at bay until MACO finish off the job. Things could turn out the other way. Even evidence Intrepid class starship more power warship then NX class.
Last possible is more simple one engine it is is expensive to build lot cheaper longer starship warp four engine.
This reason I came up with like here some others reasons though.