Command line option to override alwaysOnTop

Is there a way to override these (maybe even others) when creating a new window?

`-w -1 -M` and `-w -1 -F` are limited versions of what I want to do.

I've read a few (old) threads on specifying a settings file on the command line (valid only if creating a new window). That would seem to be the most robust way to override anything and I'm surprised it hasn't been implemented.

Another thought (hardly well thought-out) ... allow (possibly multiple) command line options like
`--option (-o) global_option_name value`, again only for new windows.

Start by reviewing the command-line option handling and the older discussions about specifying a settings file for new windows. Clarify which settings must be overridable and how repeated `--option` or `-o` arguments should behave. Done means an agreed command-line design is implemented and covered by tests for new-window creation.

Written by the indexing model from the issue text.