How to install pre bled brakes with internally routed frame
Usually what you do is disconnect it at the lever, install the lever to the bar, and run the hose up from the caliper end. Because it's sealed on the other end, no more than a few drops of fluid will escape. Then once it's through you can size the hose by turning the bars as far as they go while holding the hose up to the lever and finding the length where the hose can't get accidentally kinked. Cut it at the lever end and put on the spare barb and olive that come with the brake.

Once you have the system reconnected, in many cases you'll find there's no need to even re-bleed the brake. Since you're cutting the hose, usually the fluid will be essentially flush with the cut. Only a marginal amount of air gets introduced, and Shimano brake reservoirs are able to absorb it. (That air floats up to the reservoir in the lever and won't be in the system during braking.)

If you do want to bleed it, usually only a "gravity bleed" is all that's needed, where you skip the step of shooting oil up from the caliper and just drain it down from the cup at the lever end into the collection bag or bottle at the caliper. (Basically this is taking Shimano's written procedure and eliminating the whole first half.) The concept here is that you've only introduced air in the hose, which the gravity bleed will be well able to eliminate. 

As for whether it's really better for brakes to come pre-bled, it's probably kind of a concession to giving people something they can just put on their bike and ride without needing a bleed kit or the ability to use it, etc. It's not necessarily the best way of doing things.