The AI, most flight instruments, and engine are all permitted to be uncertified in a Permit aircraft - and therefore usually are, the vacuum system is unlikely to be duplex and the handling qualities may not have been shown to meet the standards for IMC flight, and there's probably been no consideration of lightning strike or icing in the certification ; thus flying IMC (or above an overcast) in most permit aircraft could certainly not be described as "proven safe". Yes, a good instrument pilot would probably be fine 99.99 of occasions - it's that 0.01% that will however bite somebody sometime.
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