A con? No Different reporting techniques? Possibly,
I also use Tune Up 2008 [upgraded from TU 2007 - a great bit of software IMHO] and the full version of WinASO Reg Optimizer. I used to try others and, as you post, they invariable came up with other issues that the other software had not reported.
I thought about it for a while along the lines of 'Ah! They just want you to pay' - but then, some of the software was free, so that confused me a little. Then I recall seeing a posting that some software see issues only because they are programmed to report these - whereas other pass these over as insignificant or little value in correcting.
Nowadays, I stick to just the 2 pieces and have the motto 'If it ain't broken ....'