Since we're looking at comparisons. What may be more telling is the weight increase between E39 M5 and E60 M5.
E39 M5 Manual - 3957 lb
E60 M5 SMG - 4012 lb
Weight Difference = 55 lb
Let's assume that SMG vs. manual accounts for 15lbs. that's a 40lb increase on a 3957lb car or 1.011% roughly.
Applying that to the E46...
E46 M3 Manual - 3415 lb
E92 M3 Manual (EST) - 3450 lb
Just another take on it, but only time will tell.
PS - I found a few different weights for the E39 M5 and E60 M5, but those two numbers seemed to be the most common so I went with them.