They are fast for atomics but still far, far slower than the equivalent non-atomic operation. An add operation takes around half a cycle (upper bound here - with how wide the firestorm core is an add operation is almost certainly less than half a cycle). At 1ghz a cycle is 1 nanosecond. The M1 runs at around 3ghz. So you're still talking the atomic operation being >10x slower than non-atomics.
Which should not be surprising at all. Apple didn't somehow invent literal magic here. They still need coherency across 8 cores, which means at a minimum L1 is bypassed for the atomic operation. The L2 latency is very impressive, contributing substantially to that atomic operation performance. But it's still coming at a very significant cost. It's very, very far from free. There's also no ARM vs. x86 difference here, since the atomic necessarily forces a specific memory ordering guarantee that's stricter than x86's default. Both ISAs are forced to do the same thing and pay the same costs.
How did you arrive at this number?
It's in the post. Half a cycle for an add or less, and cycles are every 1/3 nanosecond. So upper bound for an add would be around 1/6th a nanosecond. Likely less than that still yet, since the M1 is probably closer to an add in 1/8th a cycle not 1/2. Skylake by comparison is at around 1/4th a cycle for an add, and since M1's IPC is higher it's not going to be worse at basic ALU ops.
6 nanoseconds @ 3ghz is 18 cycles. That's on the slow end of the spectrum for a CPU instruction.
Separately from that x86's TSO-ish memory model also imposes a performance cost whether your algorithm needs those guarantees or not. Code sometimes relies on those guarantees without knowing it. Absent hardware support you would need to insert ARM atomics in translated code to preserve those guarantees which on most ARM CPUs would impose a lot of overhead. The M1 allows Rosetta to put the CPU into a memory ordering mode that preserves the expected memory model very efficiently (as well as using 4K page size for translated processes).