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If a module provides Panelizer defaults exported through Features there currently seems to be no good way to alter or override these other than one-off solutions.
Going through the issue queue it seems like not supporting altering feature exported Panelizer defaults was an intentional decision on Panelizers behalf. I must admit I do not understand the reason but the current situation makes it difficult to build on modules providing Panelizer defaults.
Can anybody see a way for Panelizer to support altering defaults?