One possible advantage of welding them on the inside could be it may protect the edges of the pipe from those devastating exhaust pulses. My last exhaust had the pipes sticking through the flanges maybe 1/2" into the port. It was possible to shape the 0.035 SS into an oval snugly fitting into the oval port. In the course of 100's of hours the edges of the pipe slowly got eaten away. 
 
Another reason is strees relief. The weakest point is often just next to a weld. If the pipe fits snugly through the flange the pipe is mechanically supported by the flange and not just hanging in the weld. 
 
But as other posters have commented, probably not an issue as most commercial systems are welded on the outside. 
Probably depends on thickness of material and how well the pipe is supported (also taking into consideration vibration and resonance frequencies which brings us back to looking at it with a strobelight as run run the engine and prop through its entire RPM range). 
 
Finn 
 
kenpowell@comcast.net wrote: 
 
> Hi Joe, 
> Those are really great results. I would love to know the HP > increase. Just a heads up - it looks like your new "header flange to > pipe" (picture 5) was welded on the outside. I think that 'acceptable > practices' state that there should only be a tack weld on the outside > and the actual structural weld should be on the inside. What does > everyone else say? In any event be sure to keep an eye on the welds. 
> 
> Ken Powell 
> Bryant, Arkansas 
> 501-847-4721 
> C150 / RV-4 under construction 
>  
 
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