If a block is placed on top of the capital spawn point you will spawn on top of that block rather than the set capital point. Its becomes irritating to build a capital when you cant have a ceiling.
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Not a bug, but a feature. It prevents the spawn point from being buried and covered up (a problem we had in early alpha). An open air capital square may work nicely. 
If a capital spawn point interests you, there is a project in limbo for a universal capital city on a community made planet known as the Kovah Project. When we get the world builder update where we can begin work on the project again, there will be a call for contributors. I’ll be sure to contact you then. Till then, many of us would be happy to help you build some capital spawn points! I myself would help, but I’m currently away on vacation.
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