9.2 I really need to use this in Windows with WinAVR, is it possible?

Everything is possible. You need to do the preprocessing as a separate step. Use avr-cpp to preprocess rtk.S and timer.S, and be careful not to clobber the original source files. For example, you can do the following (for timer.S):

avr-cpp -mmcu=atmega128 -DTICK_FREQ=1000 -DISR_FREQ=5000 -DTIMER_ISR=SIG_OUTPUT_COMPARE2 timer.S > timer.ss

After this step, timer.ss does not need any further preprocessing, so avr-as should be able to assemble the object file. This means you need to change the make file a little bit, and you may not be able to use the automatically generated dependency files anymore.

In essence, it is possible, but you can no longer directly use the default make files from the distribution.