When koha-create creates a new installation, it knows the URL for both the OPAC and the staff client. Why not let it update the OPACBaseURL and staffClientBaseURL syspref with the right values? This could be done with a search and replace on the SQL that is loaded from a file, or with the mechanism proposed in Bug 7426.
Because the web install portion hasn't even been done yet? There is no system preference table to populate.
That is true. Unless you specified DEFAULTSQL (in the config file) or --defaultsql on the command line. But I guess this is not that useful, so I'll close it.