It really doesn't matter what the memo says, it only matters what was on screen. And despite what the author writes. There is no showrunner who allows this to occur. Nothing, even in the 60s, was allowed on air without approval. The fact it happened so often means it was not an oversite.
This is where the "streaming" era of Trek has fallen down. Neither "Discovery" of "Strange New Worlds" jumped at the creative challenge of creating new "mission patches". At least "Enterprise" in its mirror universe episode embraced it.