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Heavy discoloration is likely to be a combination of slight overheating and normal wear material, ground off the clutch plates inside. I've worked on a couple of these A246E transaxles, and some have little discoloration, little to no debris on the pan bottom to others that are so discolored with a significant amount of shavings on the bottom of the transaxle pan.
Both ended up holding up exceptionally well. The one that had all kinds of shavings on the bottom is well on its way past 200K miles, 15K-18K miles yearly, so don't assume funky color or lots of shavings are signs of a dying transaxle (as long as the oil doesn't take on a burnt odor). The other one sees very little driving, might be less than 5000-7000 miles a year. Most are in the middle ground - some shavings on the bottom of the pan, and heavily discolored fluid.
My belief is that the friction modifiers in the Toyota Type T-IV ATF are likely the primary culprit of the discoloration issue. Keeping the fluid cooler tends to keep the discoloration from happening as quickly, but it still happens. Part of the issue is the extra weight the Matrix/Vibe has to lug around - basically the powertrain is dropped in from a Corolla, which is nearly 300lbs lighter (2568lbs vs 2860lbs). So everything has to work a little bit harder.
Auxiliary cooling is helpful, but not required. Same goes for inline filtering (some have an external filter to supplement the OEM filter "screen". Many have built in thermostats or novel designs to help make sure the fluid comes up to temperature - but there is always that risk of a leak, as you are adding many more connections in the fluid path.
Bottom line - as long as you stay ontop of fluid replacement - you should be good to go.
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2002 Corolla S, 1.8L 1ZZ-FE VVT-i
2003 Matrix XRS, 1.8L 2ZZ-GE, VVTL-i (RIP)
2009 Matrix XRS, 2.4L 2AZ-FE VVT-i
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