I think the problem you're running into is that in order to have a custom field for a post, the field must have a value. There is no sense displaying a field if there is no value for it. Depending on what you're doing, you may want to see if tags might do what you need. Where previously I was using a custom field and entering a value of 'true' to help me organize some posts that I didn't necessarily want in a full-blown category, now I just add a tag, and can view those posts on a /tag/ page, and create custom templates for that page.
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