To summarize the responses - no, "in-line" is not necessarily better, or even as good. It certainly doesn't create any sort of perfect symmetry unless many other things change. I would be curious about where you heard that, but I doubt it was from current competitive stunt fliers. As Keith noted, Bob Baron's "AVANTI" was the only successful one designed in the US in recent history, and he later claimed the Patternmaster was a big improvement.
And if you want to build a Thundergazer, stick to the original design until you have flown it enough to discover any design defects, and are able to distinguish the design defects from tiny differences in the trim, power, and construction you may have built into it. And while there is no guarantee that the design itself is perfect, the fact that it has won 5 or so NATs, a WC, and numerous other high placings in the biggest contests suggests it has no fatal design flaws. I saw it get *603* points in 20 mph winds *yesterday afternoon* as it is.
David will not respond here because he doesn't do Stunthangar, but having been his close flying buddy the entire time the Thundergazer has existed, and having flown what was maybe the 4-5th flight ever on the first one, I expect that he would say "build it however, but if you make any big changes, you are on your own".
I would recommend building it as it comes. If it is a little beyond your current skill level, then it will serve as a learning experience, but if it is way beyond your current skill level then I would suggest putting it aside and working up to it. It's not particularly hard to build by top-end stunt standards, but it's pretty complex by CL general standards, and one mistake could doom the entire project. Only you can judge for yourself.
Brett