Some scenes, esp backlit ones, can have a huge amount of polarized light from glare off of objects when the sun is close to the horizon. You can't easily use an incident meter, and the glare makes the reflected meter think the scene is much brighter than reality. Somewhat similar to taking photos in bright sun with lots of fresh snow where you meter and overexpose by a couple of stops. Rotating the pol filter for max extinction completely changes the lighting balance compared to the neutral density type light loss at minimum extinction. As you found this can give you somewhat underexposed negatives, all depends on what you are shooting.
Try metering a similar scene thru your pol filter with various angles of rotation from minimum to maximum extinction. I think you will see some major changes in the expose the meter calculates.
As an example, using a pol filter to remove the glare from the surface of a pond so you can photograph the bottom, you can't use incident metering as there can be substantial light loss from the light traveling thru the water in both directions. Besides, most incident light meters are rated as waterproof. Your only real option in this situation is ttl metering after adjusting the pol filter to remove the glare from the surface, metering thru the filter will be close, but it is awkward to do at best.