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You should have some plugs ready to go into the ports after you bench bleed and while you're installing the MC on your car. Then quickly remove the plugs and even quicklier (ha, new word), connect your lines. Do not push in the piston and release during this time and make sure there is still fluid in the reservoir while installing.
I usually install the master cylinder first and bleed while it's on the car before connecting the lines. It's the same effect as bench bleeding, but not as messy as trying to install with fluid in it.
Either way works fine, but to answer your question, yes fluid will seep out of the ports.