Regarding scale issues, in the info tab within FBX plugin parameters, (the one that opens in 3dsmax when importing a .FBX file), I've seen that file units are set to centimeters (just as you say) while system units are set to meters.
So it's no issue in the end, in the advanced options tab, inside Units parameters, "automatic" can be unchecked and choose the option "File units converted to... centimeters". That fixes and imports the file with the right scale.
There is also a tab called "Geometry" where you can check "smoothing groups" so they are preserved.
Also I'm not sure if it is really needed to offset the markings from the model, as markings mats have an offset property for them to render "on top" of skin texture. But it is sometimes annoying while editing them in 3dsMax because they fight with each other and doesn't look right in the viewports
Within the MSH file we have mesh parts. Mostly these are the main mesh, and any overlays. These use the same vertex pool through out, but use different index lists and UV pools. I have tried to re-create this in the FBX file, and failed by the look of it.
What I find interesting (I'm using CF_D0 part for the test as in your picture ) is that the model materials are recognized and have its own slot correctly assigned with unique ID, but last material (Overlay7 with ID 8 ) is missing.
ID original: test model:
1 Glass2 Glass2
2 Gloss1D0o Gloss1D0o
3 Gloss2D0o Gloss2D0o
4 Matt1D0o Matt1D0o
5 Overlay1 Overlay1
6 Overlay4 Overlay4
7 Overlay5 Overlay5
8 Overlay7
and even though the test model has the needed group of faces separated as elements, these separated elements themselves doesn't preserve ID's, their original ID are lost and all are assigned to ID 1, so only the first material (and his associated texture) is aplied to the whole model, the others materials and textures are unused.
It can be edited though inside 3dsMax, but seems like this last material and the ID assignaments for elements are missing during the exporting?
orientation of the model is not an issue "per se", can be any, but it makes very time consuming and a bit annoying if you have to rotate all the parts of the model to put them together right, and makes navigate through viewports a nightmare because labelling of viewports doesn't match anymore with orientation of the object (bottom view can be looking at the model from front, and front view is top o the model or whatever) ...and working with local and world coordinates is even more funny...
Anyway, that's a minor issue in the end, preserving original materials ID's seems maybe more important.