Ok, hopefully this works?

nbconvert/templates/latex/base.tplx

@@ -18,6 +18,7 @@ This template does not define a docclass, the inheriting class must define this.
 \listfiles
 \usepackage{amsmath} % Equations
 \usepackage{mathspec}
+\usepackage{unicode-math}
 
 \setmainfont[Ligatures=TeX,PunctuationSpace=WordSpace,Extension=.otf,
 Numbers=OldStyle,WordSpace={1,0,0},UprightFont=*-regular,BoldFont=*-bold,
@@ -28,8 +29,9 @@ Numbers={OldStyle,Monospaced},WordSpace={1,0,0},Scale=1.0,
 UprightFont=*-Regular,BoldFont=*-Bold]{SourceCodePro}
 
 \setmathsfont(Latin,Greek,Digits){TeX Gyre Pagella Math}
-% \setmathrm{TeX Gyre Pagella Math}
-\usepackage{newunicodechar}
+% \setmathfont{texgyrepagella-math.otf}
+\setmathrm{TeX Gyre Pagella Math}
+% \usepackage{newunicodechar}
 
 % Basic figure setup, for now with no caption control since it's done
 % automatically by Pandoc (which extracts ![](path) syntax from Markdown).