Theres a really easy fix to this, and i think what you're asking for is quite extreme, not something thats easily automated. I'll recap my workflow here.
After you have your highres, and lowres meshs:
Uv your lowres
Make a copy of lowres mesh
Explode copied version in low, and in highres
Save out orig version
Bake from exploded meshes
Load up the final lowres mesh in the "Simple AO tool", bake a texture the same resolution as your other textures and bam, composite this image in with the other ambocc texture, edit out the shadows on parts that need to move etc.
This could also be done with max etc if you dont like the quality of the simple ao tool for lowres meshes, i usually blur the map a little and spend a few seconds painting out errors. Also be sure to make a layer mask for parts of your mesh that would need to move, so it doesnt have ambocc on it.
Theres actually a few extra practical advantages to doing it this way as well:
1. When using floating geo, you'll often get ambocc artifacts that you need to paint out, if your mesh is exploded and you have seperate layers for high and low frequency ambocc its easier and quicker to paint out these errors that it is when you have the small shadows along with the large shadows both in the same texture.
2. Matching the exact silhouette of the lowpoly is actually a more desireable result than that of the highpoly.
Example: You have a 32 sided cylinder intersecting with some other shape, if you bake the ambocc directly from the highres you'll get a perfectly round shape. If you bake it from the lowres you'll get a shape that actually fits your model instead of just hurting the mesh by point out how jagged your lowres really is(via the contrast from the 12 sided guy casting a perfectly round shadow, not matching up correctly etc).
Heres a comp of what goes into my lightmaps for textures
1. AO from exploded
2. AO from lowres
3. 1+2 combined
4. Extra fluff, gradient baked down, NM thrown into crazy bump to create detail map, then overlayed, etc
5. Final diffuse