That would add inefficiencies to the process as well as limit investment in long term higher capability solutions in favor of playing it safe.
At this point a certain amount of customization is generally required to be made for the payloads going up. Some missions offer more flexibility than others, but generally you have to know the launch system ahead of time, not pick it after the fact.
From the launch company's perspective, they can only reach as far as they can be assured they can afford. From the investor's perspective the chance of ROI is riskier when a company has the promise of one paying job, instead of say ten paying jobs. NASA can be criticized for many things, but I'm not sure this is one of them. It's rather hard to have a buyer's market with out adequate competition. NASA is fostering the creation of that competition with the COTS and C3PO programs.
There seems to be a perception that these contract batches are the only ones that will be offered, they are not. There are plenty more contracts that will be up for bid in the future. I can guess at reasons for which Boeing was chosen over Sierra Nevada for this round but it doesn't mean Sierra Nevada is excluded from future rounds. Call it a hunch but given that SpaceX is offering the same services for almost half the cost of Boeing, Boeing probably isn't going to fare quite so well in the next round should they SpaceX succeed at delivering. Unless politicians intervene, SpaceX will be setting the bar for future contracts.