No, the power bleeder will not leave residual in the system. You fill the power bleeder with fluid and going wheel by wheel, you clear the fluid out till the clear, new fluid appears. Once you have done all four wheels you system is free and clear of all old fluid.
Your statement of "feeling" of leaving a good bit behind indicates you might not fully understand the operation of what is happening. The power bleeder is acting as the new fluid reservoir, as you flush you are pushing all the fluid out of each line separately. There is no mixing between lines. When you are done the system is refreshed with new fluid.
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