I am not an expert on this but I will give it a crack.

The rear head on the MC21 has the spark plug more centrally positioned than the front head.
The front head has the spark plug screw into it at more of an angle to give clearance between the front plug and the radiator.
By putting a rear head on the front barrel, you get the advantage of a more centrally located plug,
but you have to use the "shorty" plug and cap to clear the radiator.
You also have to use a different water hose to match the different pipe connection geometry of the rear head compared to the front head.
Also, you need to change two of the head studs. This is basically all mentioned in the engine tuning section under the heading of "Supplementary modifications"

The flow of gas up into the rear cylinder is a bit of a tortured path as it has to turn through 90º after entering the crankcase in order to go up through the transfer ports.
The front cylinder is positioned pretty much in a straight line along the direction of flow through the carbs and reeds, and even between the crankshaft webs.

So possibly, it is reasonable to take from this that the front cylinder will fill better due to better flow dynamics.
Some people will say that inside the crankcase is such a turbulent environment anyway, that it has no real effect either way.
I leave the reader to draw their own conclusions here.

But lets just ASSUME for now that for whatever reason, (suggestions welcome) the front cylinder does indeed fill more efficiently.
If this is the case, with the two cylinders otherwise identical, then the compression pressures may well be slightly higher in the front cylinder.
By positioning the spark plug more centrally, then the supposedly better burn that is achieved as a result, could possibly create a situation where the front cylinder is now effectively running at a higher state of tune.
Maybe that is not the best way to describe it, but you get the idea. Maybe its all untrue? I am open to correction/ideas here that's for sure.

So just to calm things down a bit in the front cylinder, in a simple way, without getting the lathe involved, using a 0.6mm base gasket (instead of the standard 0.5mm base gasket) gives the front cylinder a slightly lower state of tune. (This hopefully is a "relative equivalent" state of tune as the rear cylinder?)
That is; 0.1mm more squish depth, a fraction more volume in the combustion chamber and hence a slightly lower compression ratio.
Note that different jetting will also help here, and I believe that if you look it up, you will find that slightly richer jetting is recommended in the front cylinder for the "rear head conversion".

So that's about the best I can do to answer the "Why 0.6mm base gasket on the front cylinder when doing the rear head conversion" question.
Hopefully someone can improve on that. And I mean factual/explanation-wise, not get-the-lathe-out-wise.

As for recommended squish,.. well that's typically a question that results in argument on this forum.
This is probably largely due to the multiple variables involved, and differing levels of knowledge/experience/personality.
I have set my MC18 SP (road use / pump gas) to 0.8mm squish with a 12.8cc combustion volume (to the the top of the spark plug hole), but am still to do a dyno chart after about 12 months!<sigh>
Others will vary, but typically 1.0mm of squish for road use (and total vague-ness on combustion volume) seems to keep most people happy.
As a comparison, stock standard squish is in the 1.2 - 1.3mm range I believe.
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