Difference is your comparing a sportscar (Z4M) to a fast family car (M3). The M3 is a compromise the Z4M isn't really it does what it says on the tin its small had 2 seats and lack of practicality.
As fantastic as the M3s are the E92 is far from the best IMO its too big and too heavy and feels like driving a boat compared to Z4M or E46 M3. You can tell it was designed for the American market. On a hoon its good fun leaving it high in the rev range, but with little grunt lower in the rev range means dallying it is a bore and you will probably get burned up by little hatches if your not on it all the time. The S54 has 80% available from 2000rpm so feels a bit nippier.
The official figures are 0-60 in 4.8 but the M3 in manual unless the tyres are warm the conditions are correct will never do that the DCT with launch is a different story and more predictable. The Z4m is meant to be 5 dead but many have consistently got it quicker than that more like 4.8 so very similar.
Another issue with the M3 is it struggles to get the power on the road, the one we had went through tyres like no tomorrow and drank fuel like it was going out of fashion and the drive was... ok not spectacular.
Also being the odd ball I think the 4 door looks miles better than the coupe in the E9x. The rear end of the 4 door just looks amazing and you actually get more practicality with very little extra compromise and looks more of a sleeper.
In terms of the Manual vs DCT. The manual is great but to get the most out of that engine the DCT is the way to go. We had the manual and it was really fun to drive.
The best bit the noise, the V8 is amazing and its such a shame the E9X M3 was the only car that got it! Its basically a similar size and weight to the S54 its an engineering marvel. But you have to be careful they tend to have more half shaft bearing issues than the S54.
EDC is also not standard its an option and completely necessary IMO.