Difficult to say without seeing the full code.
If you toggle a digital output pin on your 25 us ISR entry and exit, and look at that with a scope, does it then ever miss a cycle?
You can also timestamping with ARM_DWT_CYCCNT, that gets you the...
Is it just with Serial6, or also Serial1, Serial2, Serial3, Serial4, Serial5, Serial7 or Serial8?
Making a PWM signal in software is maybe not the best way. Hardware timers would be better. The imxrt1062 has plenty of those.
An example for serial with DMA on T4.1:
https://forum.pjrc.com/index.php?threads/using-dma-to-store-uart-byte-directly-in-teensy-3-5.71466/#post-315706
Curt, can you share a picture on how your T4.1 is fitted in the target system? One that rules out that other electronics heats up the environment where the Teensy and its PTC sits.
Plus are you using SD cards? Some cards use very high currents...
As for why you're getting strange results, I'd like to suggest compiling your program (or a small test program) with Arduino IDE.
We regularly hear about problems with PlatformIO which turn out to be caused by using different compiler options...