Can we use a here3 gps module with rtk capability as base station instead of here+ base?
Yes, you can. But how are you planning to connect it?
To the FC? No problem.
To a PC? A little more complicated.
I have two of these here3 module. One will go on copter. Another one i want to configure as base for rtk. Can i use one more fc and connect to mission planner to send rtcm data to copter? Or any other method to get rtcm data.
Try this instead (likely the cheapest fixed base option):
There are much better modules out there, but they cost 3 times more.
You could also try a local NTRIP source. Look at rtk2go or a state run CORS service.