The height of the piston protruding from the block should be about 0.8mm or so. (You need to find this specification to be sure - 0.6mm sounds a bit low to me - but I've never taken a M104 to bits before)
3mm is really wrong - what sort of connecting rods do you have fitted to get that?
I don't think it is a good idea to remove much meat from the piston crowns to change the compression ratio. Not only do you have to make a large volume change but the engine will probably be running hotter and dealing with greater pressures - weakening isn't a great step forward in my opinion...
Here's a link for the effective compression ratio calculation =>
Effective Compression Ratio Calculator | GTSparkplugs
And here's some advise (OK for an Alfa) saying about 11:1 effective compression ratio is about enough!
Turbo and Supercharged Engine Compression Ratio Calculator
I've seen threads where people have said they have added turbos to M102s and such with 0.5 to 0.8 bar boosts but these people don't seem to stick around for long!
A M104 has a 10:1 compression ratio which means about 4PSI / 0.27 bar is about the most that will possibly work with petrol to give you an effective compression ratio just about 11:1 (this might be too much)
You can calculate the additional volume in the cylinder if you want to lower the compression ratio by fiddling around with the formulas in this thread =>
http://www.peachparts.com/shopforum/diesel-discussion/293139-does-anyone-have-any-nifty-ways-measuring-true-volume-engines-cylinder.html
Alternatively this might help
Not2Fast: Compression Ratio Calculator