Everything you said is more or less correct. Despite these shortcomings, the 460 cylinder still works amazingly well. It's a case of "nearly perfect" compared to other options which were even more involved.I was under the impression the yd100 rod still leaves the stroke just shy of what it should be.. I know the geometry is totally different from saw to cg cranks and another thing I found out was if you mill the cylinder down to get stihls squish specs you end up going like 1mm too much and at tdc the exhaust port is slightly open below the piston skirt.. something about using the rod from a Husqvarna 760 cut saw.. good luck finding just the rod.. crank assembly is around $350-400.. I'm hard pass on that one.. but if you find someone with a few of them laying around, I needs one.. but as far as port timing goes.. idk.. Im pretty sure it would probably need some finessing to get it dialed in properly.. lol. Properly.. if that word even belongs in the same category as chinasaw.. but, if I'm not mistaken, I think it's the ms260 or 290.. there's no rod swap needed and the 48mm bike motor piston will work with a 1mm spacer to lift the cylinder.. again, Im just going by what I halfway threw together out of curiosity with a trash cylinder I had laying around. Ended up buying the ms660 54mm kit instead of the 48..
That is why the Phantom cylinder was made. It corrects the main issues, such as the exhaust port, and gives a bolt on solution so that no machine work is required. The only real change made outside of port position corrections to work on the yd bottom end was the size and shape of the intake port, converting it to flange for the 40mm intakes, and making it smaller at the flange to - I presume - reduce the power output a little bit.
I own a 460 saw and have a cylinder left over from a rebuild. If you place them side by side you can see the changes that were made, but also just how nearly identical they are.