Alter fonts to make ascent=descent so that line-height:0 makes its axis along the baseline. That should simplify things (though it may make unknown characters harder to handle -- we'll see).

unpacked/jax/output/CommonHTML/fonts/TeX/fontdata.js

@@ -586,8 +586,6 @@
 
   CHTML.FONTDATA.FONTS['MathJax_Caligraphic'] = {
     directory: 'Caligraphic/Regular',
-    ascent: .789,
-    descent: .216,
     skew: {
       0x41: 0.194,
       0x42: 0.139,
@@ -659,8 +657,6 @@
   CHTML.FONTDATA.FONTS['MathJax_Main-bold'] = {
     directory: 'Main/Bold',
     weight: 'bold',
-    ascent: .951,
-    descent: .267,
     skew: {
       0x131: 0.0319,
       0x237: 0.0958,
@@ -797,8 +793,6 @@
   CHTML.FONTDATA.FONTS['MathJax_Main-italic'] = {
     directory: 'Main/Italic',
     style: 'italic',
-    ascent: .750,
-    descent: .250,
     Ranges: [
       [0xA0,0xFF,"Latin1Supplement"],
       [0x300,0x36F,"CombDiacritMarks"],
@@ -910,8 +904,6 @@
 
   CHTML.FONTDATA.FONTS['MathJax_Main'] = {
     directory: 'Main/Regular',
-    ascent: .900,
-    descent: .272,
     skew: {
       0x131: 0.0278,
       0x237: 0.0833,
@@ -1192,8 +1184,6 @@
   CHTML.FONTDATA.FONTS['MathJax_Math-italic'] = {
     directory: 'Math/Italic',
     style: 'italic',
-    ascent: .717,
-    descent: .218,
     skew: {
       0x41: 0.139,
       0x42: 0.0833,
@@ -1372,8 +1362,6 @@
 
   CHTML.FONTDATA.FONTS['MathJax_Size1'] = {
     directory: 'Size1/Regular',
-    ascent: .850,
-    descent: .350,
     0x20: [0,0,250,0,0],               // SPACE
     0x28: [850,349,458,152,422],       // LEFT PARENTHESIS
     0x29: [850,349,458,35,305],        // RIGHT PARENTHESIS
@@ -1423,8 +1411,6 @@
 
   CHTML.FONTDATA.FONTS['MathJax_Size2'] = {
     directory: 'Size2/Regular',
-    ascent: 1.360,
-    descent: .862,
     0x20: [0,0,250,0,0],               // SPACE
     0x28: [1150,649,597,180,561],      // LEFT PARENTHESIS
     0x29: [1150,649,597,35,416],       // RIGHT PARENTHESIS
@@ -1466,8 +1452,6 @@
 
   CHTML.FONTDATA.FONTS['MathJax_Size3'] = {
     directory: 'Size3/Regular',
-    ascent: 1.450,
-    descent: .950,
     0x20: [0,0,250,0,0],               // SPACE
     0x28: [1450,949,736,209,701],      // LEFT PARENTHESIS
     0x29: [1450,949,736,34,526],       // RIGHT PARENTHESIS
@@ -1493,8 +1477,6 @@
 
   CHTML.FONTDATA.FONTS['MathJax_Size4'] = {
     directory: 'Size4/Regular',
-    ascent: 1.750,
-    descent: 1.250,
     0x20: [0,0,250,0,0],               // SPACE
     0x28: [1750,1249,792,237,758],     // LEFT PARENTHESIS
     0x29: [1750,1249,792,33,554],      // RIGHT PARENTHESIS

unpacked/jax/output/CommonHTML/jax.js

@@ -34,8 +34,7 @@
   var EVENT, TOUCH, HOVER; // filled in later
 
   var SCRIPTFACTOR = Math.sqrt(1/2),
-      AXISHEIGHT = .25,
+      AXISHEIGHT = .25;
-      HFUZZ = .05, DFUZZ = 0;  // adjustments to bounding box of character boxes
 
   var STYLES = {
     ".MathJax_CHTML_Display": {
@@ -558,14 +557,8 @@
       }
       this.addCharList(node.firstChild,list,bbox);
       this.cleanBBox(bbox);
-      bbox.h += HFUZZ; bbox.d += DFUZZ;
+      node.firstChild.style.paddingTop = this.Em(bbox.h);
-      bbox.t += HFUZZ; bbox.b += DFUZZ;
+      node.firstChild.style.paddingBottom = this.Em(bbox.d);
-      var a = (bbox.H-bbox.D)/2;  // center of font (line-height:0)
-      if (a < bbox.h) {node.firstChild.style.paddingTop = this.Em(bbox.h-a)}
-        else {node.firstChild.style.marginTop = this.Em(bbox.h-a)}
-      // ### FIXME: Safari doesn't center, so clip bbox.d at 0 and adjust later?
-      if (bbox.d+1 > 0) {node.firstChild.style.paddingBottom = this.Em(bbox.d+a)}
-        else {node.firstChild.style.marginBottom = this.Em(bbox.d+a)}
       return bbox;
     },