Placing the lines back into the MC is the standard method I've always seen in manuals and intructions included with replacement MC's, And, I do agree that aerated brake fluid can be a factor in the process. While bleeding into a separate container, make sure the hose end remain below the bled fluid level to prevent any air being sucked back into the MC. You may need to put a small amount of fluid in the container at the start of the process.
