Two quick answers:
Yes. In fact, this is the expected behavior. Bundles are designed to create a seamless installation experience. Providing a single user interface in your BootstrapperApplication is part of that.
No. The BA does not run elevated so it cannot modify machine state. If you are changing the machine, it should be part of the transaction in an MSI. The BA should only be responsible for interacting with the user (aka: take input, show progress, etc).