BoringUtils + when/layer/region produces invalid FIRRTL

**Type of issue**: Bug Report

**Please provide the steps to reproduce the problem:**

Consider these tests: https://github.com/dtzSiFive/chisel3/commit/d8a3f1213c32a9e69fd6e15eaf4c9030ce2235fb .

Steps to reproduce are to checkout that branch / apply that commit and run the tests.

**What is the current behavior?**

The tests fail due to generating invalid FIRRTL because BoringUtils appends connect statements to the end where not all declarations are visible.

Example FIRRTL for the layer test example:
```
FIRRTL version 4.0.0
circuit Top :
layer TestLayer, bind : @[src/test/scala/chiselTests/BoringUtilsTapSpec.scala 167:36]
module Bar : @[src/test/scala/chiselTests/BoringUtilsTapSpec.scala 168:11]
output out : UInt<1> @[src/test/scala/chiselTests/BoringUtilsTapSpec.scala 169:19]
input out_bore : UInt<1> @[src/test/scala/chiselTests/BoringUtilsTapSpec.scala 170:36]

connect out, out_bore @[src/test/scala/chiselTests/BoringUtilsTapSpec.scala 170:11]

module Foo : @[src/test/scala/chiselTests/BoringUtilsTapSpec.scala 172:11]
input out_bore : UInt<1> @[src/test/scala/chiselTests/BoringUtilsTapSpec.scala 170:36]

layerblock TestLayer : @[src/test/scala/chiselTests/BoringUtilsTapSpec.scala 173:30]
inst bar of Bar @[src/test/scala/chiselTests/BoringUtilsTapSpec.scala 174:25]

connect bar.out_bore, out_bore @[src/test/scala/chiselTests/BoringUtilsTapSpec.scala 170:36]

public module Top : @[src/test/scala/chiselTests/BoringUtilsTapSpec.scala 177:11]

wire parentWire : UInt<1> @[src/test/scala/chiselTests/BoringUtilsTapSpec.scala 178:28]
inst foo of Foo @[src/test/scala/chiselTests/BoringUtilsTapSpec.scala 179:23]
connect foo.out_bore, parentWire @[src/test/scala/chiselTests/BoringUtilsTapSpec.scala 170:36]
```

`connect bar.out_bore, out_bore` is invalid, `bar` is only visible within the layer.

**What is the expected behavior?**

Boring produces diagnostic instead of illegal FIRRTL (as reasonable), and for probes this should work.

**Other Information**

Encountered this migrating to boring probes, specifically involving a layer.

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