Pages equations are MathML objects embedded in the document. If you select one and change the current font size, the object will respond in size accordingly. Other fonts, depending on their inherent line heights may increase or decrease the equation object size, but will not apply the font characteristics to the equation contents.
I recommend a read of the blahtex translator support which is what converts Equation Editor entries from TeX/LaTeX/MathML syntax to MathML Pages equation objects. There is a link to the blahtex PDF in the following article:
About LaTeX and MathML support in Pages, Numbers, Keynote, and iBooks Author - Apple Support