> Then how do you propose those using it, as lets say in my example, set the 
> cgi directory for that vhost?

They can keep using it, get the equivalent function from a default
configuration and never be the wiser,  or use/change to Alias + an
explicit  SetHandler and Options.
Most default configurations already have both the ScriptAlias and a
Directory section that matches the 2nd argument of the ScriptAlias.

> ScriptAlias's purpose is to say hey httpd, our https://domain/cgi-bin/ 
> directory is really here on the filesystem at /var/www/cgi-bin/
> Its simple and works for decades, if you feel its not sure and needs 
> replacing with other commands, the code for other commands should be 
> internally called by ScriptAlias directive

As the manual says, ScriptAlias is equivalent to (syntactic sugar for):

Alias "/cgi-bin/" "/web/cgi-bin/"
<Location "/cgi-bin">
    SetHandler cgi-script
    Options +ExecCGI
</Location>

Rather than

Alias "/cgi-bin/" "/web/cgi-bin/"
<Directory "/web/cgi-bin">
    SetHandler cgi-script
    Options +ExecCGI
</Directory>

Generically, we tell people to use Directory sections when they think
they're working with filesystem content so some unexpected URL to
filesystem mapping can't have an unexpected result.
ScriptAlias subtly exposes you to this same kind of problem for
marking resources to be interpreted as CGI.

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