That's what I was thinking.
PvE-only ships would need to be "ghosts" in order to entirely prevent them from interfering with other player-ship activities.
What happens if I am, say, trying to collect black boxes for a mission* and a "PvE only" ship decides to interfere?
With all this PvE-only malarkey, another ship could, presumably ram or shoot the black boxes, it could get in the way and generally become a nuisance and there'd be nothing I could do about it.
The only way to prevent this completely would be to make the other ship completely intangible, so it's weapons couldn't damage the black boxes and my limpets, and I, could both fly through it.
And this wouldn't be immersion-breaking?
*This has happened to me in the past, with some yahoo following me around and exploding every black box I tried to collect.
TBH, it was kind of fun trying to outwit/outfly the other guy, even though he was probably trying to "grief" me.