Re: making holes
Another approach could be to compose the sides of multiple column/row strips (instead of cutting out a single face). You could compose one "row" or "column" of your pergola side, then copy and paste it multiple times until you have enough to compose the entire side.
I'd do this with grid snap enabled - this way, once you've finished, you could merge the strips into one object and remove duplicate vertices if you wanted to.
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