[toplevel] Allow to specify default options.

In some cases, toplevel ML clients may want to modify the default set
of flags that is passed to the main initalization routine. This is for
example useful for `idetop` to suppress some undesired printing at
startup.

I would say that clients ought to have more control, but I do expect
that PRs such as #8690 will help providing a better separation thus a
mode orthogonal API.

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