Hi again Hermann,
You are right estimating the frequency of the signal generated with the Pi using the average, specially if the signal has no constant frequency and period. But to know really until which frequency is possible to use the DUE (the ATSAM3X8E), and in turn, tc_lib, would be interesting to try to feed it with a PWM constant signal. Wouldn't that be possible using the Pi?.
In relation to provide tc_lib with the ability to measure average frequencies and periods, it is easy to do it using tc_lib as it is, you only have to accumulate the readings of periods and frequencies in an array. The thing is tc_lib was devised to measure pulse duration (duty) and period of digital signals, not necessarily constant, in an instantaneous way. In this manner you can measure instantaneous velocities of rotary axes of motors, etc.
Best.