Nope.

https://cruxnow.com/global-church/2016/12/24/knights-malta-pope-stay-internal-affairs/

Think about it by comparing it to another soverign catholic instiuttion, a private Catholic school.   A private Catholic school is sovereign in its administrative decisions. 

The only oversigtht the Church, including the pope has with this sort of school is whether its Catholic related teaching..including on matters of faith or morals is in line with Church teaching.

The Church can't put its nose into the administration of such a private Catholic school, that is to say a non-diocescean school.

the lay order of malta...same thing.  

It does'n't fall under the governance/rule of any Congregation.