…the linker configuration.

Also call Application.InitializeCommon to initialize the application instance. The
important part here is that InitializeCommon calls Optimizations.Initialize to compute
the default optimizations. It also calls Set*ExceptionMode and sets the default EnableCoopGC
value (so we don't need to call/set those anymore), and it does a few other initialization
tasks which we don't need yet, but eventually will.

And finally remember to parse the bundler arguments before using them in the dotnet
build logic. How did this not cause problems before? 🤦

…ernal variable.

The internal _BundlerVerbosity variable is overwritten now (with the verbosity
value from the additional args).

…t incorrect and needs fixing.