They do. The problem is that you think the ISR and RPI are gospel in telling us who the best team is instead of telling us who had the best season, which is what those programs actually do.
No they don't.
We can use any measure you want too.
# 1 National seeds are 1-for-17 in winning the national championship (Miami in 1999 was only winner).
# 2 National seeds are 2-for-17 in winning the national championship (LSU in 2000 and Miami in 2001).
# 3 National seeds are 1-for-17 in winning the national championship (LSU in 2009).
Notice a trend?
And the ISR
does purport to tell us who the best team is. I know this because I actually read and follow Boyd Nation.