As far as I know you can't. The code that is used in Beyond Earth is different from the code in Civ 5 and uses a different (simpler) method, there is no way to make a building "invalid". So you'd need to rewrite CityView.lua yourself to manually create an exception for your buildings - that could cause a lot of compatibility-issues though.
I've simply been using visible buildings to implement stuff for a while now though and I've not had any complaints. I usually just put a descriptive text into the buildings Help-Tag to make sure people know where they got that building from.
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