configurable-file-extensions: Shadowing addon files doesn't always work

Cross-posting from #topic-typescript, so it doesn't get lost:

I noticed a peculiar problem with https://github.com/babel/ember-cli-babel/pull/140. I’m shadowing / clobbering files in the `app` directory provided by addons. For example, ember-intl re-exports the `intl` service and `t` helper in their `app` directory. I’m shadowing these with my own compatibility layer `intl` service and `t` helper. I’m doing the exact same thing to the `features` service of ember-feature-flags. This used to work reliably with ember-cli-babel 6.

But now it seems that _sometimes_ this shadowing does not work and the addon-provided files “leak through”. I’m also unable to find my override file in the Chrome Dev Tools. Triggering a re-build on the “missing” file by `touch`ing it fixes the problem.

Does it maybe have something to do with parallelization?

Concretely what happened is that my `t` helper was sometimes missing and the ember-intl one leaked through. Same happened to the `features` service.

One side-note: I’m using my https://github.com/babel/ember-cli-babel/pull/236 branch to process `.ts` files.

This might be part of the cause.