[bootstrapper] Refactor CreateFunction and InstallFunction.

Move set_native(true) from InstallFunction into CreateFunction in order to
emphasize the places where we create non-native functions.

No change in semantics overall.

BUG=

Review-Url: https://codereview.chromium.org/2667993005
Cr-Commit-Position: refs/heads/master@{#42854}