I found a while back that if you run a thin blade over the lighter lines to break the surface, most of the time a thinned out varnish will be able to access the cells that are 'sealed' and you'll get most of the colour you're aiming for. Depends if you want to spend the time on it though. 
Personally I don't mind it that much, depending on the colour of the floor. I just looked at the wooden floor underneath me and I can pick up plenty of places where the timber has lighter streaks through it. It's a naturally occurring thing. Again, colour choices determine the 'type' of timber though, and old castle hardwoods would be less likely to have this I guess.