On colder days rain or not, I often wear less or thinner layers and just wear a rain jacket as a wind breaker.
Knowing the rain jacket can make you hot by reducing airflow.. I plan on that and use that to my advantage.
If no rain
I wear a base layer, rain jacket, then a top layer. I'll take off the top layer at any point if I start getting hot (that decision is obvious after I warm up and get going a few miles). I'll make further adjustments with a few inches of the jacket zipper as needed.
If rain starts
I'll put the top layer on under the rain jacket or just leave it off.

Sounds complicated but it's really not. I plan my clothes in the cold assuming I'll be wearing the rain jacket the whole time and adjust other layers instead. Maybe people have these super great rain jackets but none I have ever owned can breath good enough to simple put on and take off without a drastic change in body heat retention one way of the other.