Mixing ChiselStage with ChirrtlEmitter does not work in 3.4.0-RC2

**Type of issue**: bug report

**Impact**: no functional change

**Development Phase**: request

**Other information**

**If the current behavior is a bug, please provide the steps to reproduce the problem:**

**What is the current behavior?**

Scastie link: https://scastie.scala-lang.org/BhBOK32BQRmzZLMH71tAfw

Given:
```scala
class MyModule extends Module {
val io = IO(new Bundle {
val in = Input(UInt(8.W))
val out = Output(UInt(8.W))
})
io.out := io.in
}

object MyMain extends App {
val annos = List(
ChiselGeneratorAnnotation(() => new MyModule),
TargetDirAnnotation("dir"),
RunFirrtlTransformAnnotation(new ChirrtlEmitter)
)
(new chisel3.stage.ChiselStage).execute(args, annos)
}
```

Crashes with:
```
firrtl.options.PhaseException: Multiple CustomFileEmission annotations would be serialized to the same file, '/tmp/scastie2658337669388794900/dir/MyModule.fir'
- first writer:
class: firrtl.EmittedFirrtlCircuitAnnotation
trimmed serialization: EmittedFirrtlCircuitAnnotation(EmittedFirrtlCircuit(MyModule,circuit MyModule :

- second writer:
class: chisel3.stage.ChiselCircuitAnnotation
trimmed serialization: ChiselCircuitAnnotation(Circuit(MyModule,ArrayBuffer(DefModule(MyModule@35ec0a6b

at firrtl.options.phases.WriteOutputAnnotations.$anonfun$transform$1(WriteOutputAnnotations.scala:54)
```

The fundamental issue is that both Chisel and ChirrtlEmitter want to write the same `.fir` file. In the past, we just wrote it multiple times and never noticed. The new `CustomFileEmission` API is stricter about this sort of thing so now it's an error.

**What is the expected behavior?**

It should either report a clean and precise user error, or better yet it should handle this gracefully.

**What is the use case for changing the behavior?**

Better user experience.