For MAX32660 and MAX32650, it is possible to use an external clock, but only up to 50MHz max, through the XTALO pin, by disabling the RTC crystal oscillator. Using 16.384MHz, should be fine.
Regarding the timer input pins on these parts: The MAX32625 is restricted to 1/4 th the peripheral clock. There is no such restriction on the MAX32650 or MAX32660 -- the timer input pin can go up to the peripheral clock speed.
The ¼ timing issue is only for timer input on the MAX32625. As output to, say, an ADC, it is not limited in the same way since the MAX32625’s maximum peripheral frequency is sysclock.