True, there's more power to move away from the junction. But the lower thermal resistance reduces the temperature rise on the more thermally efficient chip. As an example, here are the numbers at 50A.
IRFB3077 power dissipated = 50A x 50A x .0033 ohm Rds-on = 8.25W
IRFP2907 power dissipated = 50A x 50A x .0045 ohms Rds-on = 11.25W
So far it seems like the IRFB3077 will run cooler due to the lower power level that needs to be dissipated (due to the IRFB3077's lower Rds-on value). But, what is the actual junction temperature rise?
IRFB3077 junction temp rise = 8.25W x 0.9C/W = 7.43C temp rise at the MOSFET junction
IRFP2907 junction temp rise = 11.25W x 0.56C/W = 6.30C temp rise at the MOSFET junction.
Due to its much lower thermal resistances, the IRFP2907 will actually run cooler than the IRFB3077 even though the IRFP2907 has a higher on-resistance. Other factors can change this, like gata capacitance which might slow down one or the other MOSFET (heating it up more), but it's often more complex than selecting the lowest on-resistance MOSFET when trying to keep a controller running cool.
IMHO, it's a combination of two factors that blow out controllers; over-voltage and over-temperature. Since protecting against over-temperature is a lot more expensive, I agree with you that over-temperature is probably the leading cause of MOSFET failure in a controller. Especially since so few controller designers know much about calculating the thermal efficiency of their products or even how to properly measure the case temperature of an operating MOSFET.
Sil-Pads, and other silicone or rubberized thermal pads, have HUGE thermal resistance ratings! Hardcoat anodizing the heat sink is the way to go for achieving insulation between MOSFETs. But, it's much more expensive than using those pads. Using too much thermal compound is another frequent sin. Add onto that the fact that most MOSFETs are mounted with screws (not clips), which often raises up one end of the MOSFET, and it gets even worse. And as a final blow to the health of those poor MOSFETs, they don't even use Belleville washers under the screws. This allows the screw to loosen over time due to thermal cycling and the MOSFET is then not firmly against the heat sink.
The life of a controller MOSFET is a tough one.