the Battenbergs and Mountbattens are not a junior branch but a morganatic branch of the House of Hesse.
there are however various other (former) reigning dynasties who have several branches reigning in different countries.
Glucksborg is reigning in Denmark, but also in Norway and another branch reigned in Greece. The house itself was a branch of the Oldenburg dynasty that reigned in that duchy also.
The House of Saxony has/had various reigning branches:
Kingdom of Saxony
Grand Duchy of Saxony Weimar Eisenach
Duchy of Coburg
Kingdom of the Belgians
Kingdom of Bulgaria
UK and India
plus the kingdom of Portugal (1853-1910)
the duchy of Saxe-Meiningen
the duchy of Saxe-Altenburg
Parma and Piazenza
The oldest branch reigns in Luxemburg a junior branch in the Netherlands both dynasties have continued in the female line.
Even though there are several members of the Saxe-Coburgs on thrones or pretenders to thrones, I understand that this family is actually a junior branch of another royal family- Wetton,
perhaps? Is the royal family of Romania members of a junior branch of the Hohenzollerns?
As a matter of fact, a junior branch of the Hohenzollern-Sigmaringen, a junior branch of the Hohenzollern family whose senior branch reigned in Prussia.
Are the Mountbattens in somewhat the same position as well?
The Mountbattens are a junior (and non-dynast in Germany) branch of the Hesse-Darmstadt, a junior branch of the Hesse family, itself a descendant of the Brabant dynasty.