Yes, both those documents have been mentioned earlier in this thread, and have been studied by the original poster.
The original poster have also spotted that TABLE 9-1: Clock Distribution,
have no mention of QEI quadrature decoder,
so this table may have been copied from a similar device without a QEI peripheral.
Figure 30-1: QEI Block Diagram in datasheet for PIC32MK,
there is PBCLK2 feeding in to QFDIV divider, and then into filter logic.
In the corresponding figure in FRM48,
Figure 43-2: Quadrature Encoder Interface (QEI) Module Block Diagram,
there is unspecified PBCLK that feed into QFDIV divider, and then in to filter logic.
In Figure 43-9: Block Diagram of Digital Noise Filter,
there is a TCY
appearing from the left, feeding the first latch, and QFDIV divider for clocking the shift register.
Now, there is the general definition, that if there are difference in details
between FRM document and Datasheet for a specific device type,
then it is Datasheet that shall have authority.
I would be highly surprised, if this TCY
were any different from PBCLK2 in PIC32MK...
This may be checked by setting: PB2DIVbits.PBDIV to it's highest value, giving the largest divisor,
QFDIV to a suitable value, FLTREN to 1,
and then test what frequency of input signals the quadrature decoder is able to resolve correctly.