The bounding box in MathType adds some padding to the equation. It can be adjusted somewhat via a registry setting:
BUT, there is the problem, if you make the registry edit, then clipping is likely. And EVEN if it is not clipped, the bounding box size is set up for full size (caps) of a font. For example, the bounding box is fit to "Z" instead of "z". This makes it difficult to control the spacing of the equations in ID.
So I a few options:
1. Manually adjust the bounding box (clip) inside of ID. For hundreds/thousands of equations this does not seem like much fun and huge time expense.
2. Develop a script or something? This could either be done in MathType (somehow I doubt it) or more likely done with a script on the actual EPS itself. I am exporting to EPS for just this reason already (since I do some processing to the EPS that MathType can not do).
3. Any other ideas? Could ID do something clever? Perhaps I am missing a simpler opportunity?
I can't help you! I have no problem with MathMagic I use.