That looks like a cut-and-paste bug when those manuals were being assembled.
Searching shows those register and bit names only exist in the MCF5329 and MCF5373 manuals, so it doesn't immediately look like a chapter got pasted from an MCF52xx chip as I've seen before.
"bits 2,3,4 and 5 being used in the PODR_PWM, PDDR_PWM and PPDSDR_PWM" have been named as per the bits in that register, which is consistent for that chapter.
The PWM signals are named for their function.
I think the "proper fix" would be to change only the second column in "Table 2-1. MCF5327/8/9 Signal Information and Muxing" and "Table 13-1. MCF5327/8/9 Signal Information and Muxing" to something like:
Signal Name GPIO
--------------------
PWM7 PPWM5
PWM5 PPWM4
PWM3 PPWM3
PWM1 PPWM2
Please write some code totest this out and then report back.
Tom