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I'm not able to run your example at the moment, but it is very helpful that you provided it.

The key parameter here is combination_method. You have it set to 0, which means overwrite. This means that whatever data is in the obstacle layer will be written into the master costmap, regardless of what is already in the master from the static costmap.

Try setting it to 1 for Maximum, which will combine the values.

Alternatively, you can set track_unknown_space to true so that only the values which your obstacle layer has marked as clear/occupied will be copied over.