Why not? We do on two strokes that are radically different than stock configuration. They are little or no use on the open road or under stop start conditions because they are too hard to read safely on the move, but are a place to start from. The bung comes with a block off screw for normal use.
A better solution is dyno time. We jetted a highly tuned RD350 recently and took it to the dyno and it ended up with different jets in each side, and only 1 size different to where we started. That bike had a set of polished stainless pipes from Europe, so there was no way we were going to put a bung in those. So it came down to static running, street run and the dyno to get it spot on.