As far as I know, the MXA boxes are just updated MSA boxes. They may have bulkier aluminium housings, but the ratios match. My MSA clears an LT230 but I can confirm Bush65 not being able to use an LT230 with his 6 speed box. I think he went to an ATLAS transfer.

Haven't heard of any intentional bonnet mods. I had an unintentional one resulting from a thermo switch which protruded out the top of the thermostat housing further than it should have.
I managed to lower it by about 15mm by breaking the pins off and soldering directly to it. No problems since.