Just done the test with mega board and version 15 running on my Macintosh.
I confirm timer5 works perfect, here is my code where I generate 799,92Hz freq, PWM of 75% on OC5B and PWM of 1% on OC5C with clock system, phase & freq correct PWM
int outputPsuB = 45; // Timer5-B
int outputPsuC = 44; // Timer5-C
// PSU outputs via timer5
pinMode(outputPsuB, OUTPUT); // select Pin as ch-B
pinMode(outputPsuC, OUTPUT); // select Pin as ch-C
TCCR5A = B00101001; // Phase and frequency correct PWM change at OCRA
TCCR5B = B10001; // System clock
OCR5A = 10000; // 799,92Hz
OCR5B = 7500; // 75%
OCR5C = 100; // 1%
i've tried pre-scaling to diminish frequency and works perfect.
For me it looks 16-bits timer3, timer4 & timer5 are fully compatible with version 15 on Macintosh.
I'll look later on timer1 issue you've raised on your doc :-/