"Segregated" has a specific, value-neutral meaning, but it also carries social-historical baggage. It's perfectly possible to use it with a value-neutral intention, but it isn't really possible to use it without the hearer being reminded of the baggage.
I agree, and while I've tried to use the term in a value-neutral way, the effectiveness of my communication was limited by the social-historical baggage.
I usually have to speak my way around to the same meaning, by saying "separation by vehicle type" and describe the means of designating the separation, be it my markings or physical barriers. I think "separation by vehicle type" is the clearest and most accurate description, because the markings and laws involved in such separation focus on vehicle type rather than vehicle users or their relative speeds and destinations. This makes such traffic engineering fundamentally different from most other engineering of vehicular traffic patterns on typical streets.