Unfortunately, no you cannot use the 'regular' FTMx_CHy pins for index -- the FTM blocks that HAVE the quadrature-decode-mode only HAVE two direct timer-input-pins, and those must be your PHA/B inputs.
I haven't seen here where you give an exact K10 part #, so I can't verify these options, but K10P144M120SF3RM.pdf has this to say:
3.8.2.7 Input capture options for FTM module instances
The following channel 0 input capture source options are selected via SIM_SOPT4. The
external pin option is selected by default.
• FTM1 channel 0 input capture = FTM1_CH0 pin or CMP0 output or CMP1 output
• FTM2 channel 0 input capture = FTM2_CH0 pin or CMP0 output or CMP1 output
as set in SIM_SOPT4 18/19 and 20/21. Just use a 'nice' center-trip-voltage for the comparison-voltage (internally set) to give you a nominal 'digital input'-like function. And that comparator-output will then be the 'channel 0 input' for the 'channel 0' logic of the associated FTM (figure 40-1, same pdf), and in which you can set the edge to capture, OR enable the 'dual edge mode' using both channels 0 and 1, so you have the count at both edges in C0V and C1V -- and from THAT and the 'direction' you pick up on an interrupt to read said channel(s) you can decide which edge you will 'pick' (assuming your index-width might span more than one PHA/B edge).
And yes, this all works VERY well. My interface is to a large linear-encoder, capable of >25Medges/sec, and I find this index gets me the EXACT count out 'past 1M/sec'--far faster than where one usually is 'looking' for said index-alignment signals. I expect this 'indirect path thru a comparator' incurs a delay on the order of 100ns, so somewhere around 10Medges/s we would get 'behind' an edge.
Unfortunately, said encoder also spans 1M counts, so extending the limited 16bit count is irritating.