One of the things you want to avoid in an exhaust system design, is for the pressure pulse when a given exhaust valve starts opening to travel down that cylinder's header pipe and backwards up an adjacent header pipe and arrive at that cylinder's exhaust valve just before it closes. It will cause a reversion pulse.
Whether you have 2 cylinders grouped, or 3 cylinders with even firing spacing grouped, in either case there is no (or negligible) overlap in the exhaust strokes. Even if you are using a really wild long duration camshaft, the length of the header pipes (if set correctly) combined with the speed of pressure wave propagation will ensure that the bad reverse pressure wave won't arrive at that adjacent cylinder at any plausible engine RPM in which the engine is making power. (It might happen with the engine at or just above idle speed, but for a performance engine ... who cares.)
So, that would suggest no first-order advantage of the hard-to-package evenly-spaced (360 degrees between firings) 6 into 3 arrangement, over the dead-simple-to-package (240 degrees between firings) 6 into 2 arrangement, or for that matter, the easy-to-package 6 into 3 arrangement with adjacent cylinders paired (240 then 480 degrees between firings on the outer pairs and 360 degrees between firings on the center pair).
A log manifold with all 6 cylinders into one will have overlapping exhaust pulses into that log at practically all engine speeds. A 6-into-1 or a 6-into-2-into-1 with short header pipes might have overlapping exhaust pulses at lower engine speeds depending on the length of the header pipes compared with the local speed of sound / pressure wave propagation, etc.
Bottom line is that you have to use theory to get the primary pipe lengths and diameters in the ballpark and then test, test, test.