About nine or so years ago Rav Ovadia Yosef said he feels it is wrong that many Sephardim have accepted what was an Ashkenazic-only takana against having a second wife, and said Sephardim shouldn’t abide by such an across-the-board rule.
Gaon, what you’re quoting is part of the kesuba of many Sephardim. That has been done for many years by many Sephardim but it has never been an across-the-board provision accepted by all Sephardim. The Sephardim customize their kesubas and some take certain conditions, as agreed upon between chosson and kallah prior to marriage, while other Sephardim don’t implement those provisions in their kesuba (in which case he could take additional wives without anyone else’s reshus.) But even the kesuba provision you quoted, for those Sephardim that use that provision, (as you said) even they can take a second (or third) wife with the reshus of beis din, which the provision expressly allows for.
Neville’s question was about a situation where a Sephardi was in a marriage where the wife ran away without accepting a Get or something. In such a case it would be very easy for a Sephardic Beis Din to allow him to take a second wife, due to such a circumstances. Because the provision even allows Beis Din to allow additional wives when he’s still happily living with his first wife.
An interesting point regarding Neville’s question, whereas Ashkenazim are prohibited from forcibly divorcing a wife against her will based on Cherem Rabbeinu Gershom, Sephardim have no such preclusion and could simply divorce her against her will if she took off and didn’t want to accept a divorce.