Sorry, in order to understand this a little more information is needed. When you say you are "taking the filter into account," what literally are you doing? For example some possibilities:
Example 1. TTL metering through the filter: I am setting the camera's iso at 50, putting an R72 filter on the lens, and exposing at whatever the camera's meter says to do.
Example 2: TTL metering w/o filter: I set the camera at iso 50, meter without the filter, set the exposure, then screw the filter on the lens and shoot.
Example 3. Filter factor: I am setting my separate light meter (like your Sekonic) at iso 50, metering without the filter, and then applying a 3 stop filter factor when transferring the exposure from meter to camera.
Example 4. No filter factor: I am setting my light meter at iso 50, metering without the filter, and transferring the exposure directly to camera w/o filter factor. (That's what I think you said above, but just trying to be sure.)
Example 5. Non-TTL metering with filter: I'm holding the filter in front of the light meter to take the reading before putting the filter on the lens, etc.
This may be belaboring the subject, but these examples wind up with different effective ISOs, and you have both a TTL and a non-TTL meter, so it's hard to know exactly how your process might be the same or different as other users. As far as I know, the usual ISO 6 advice builds the filter factor in for non-TTL metering (like example 4, but setting the non-TTL meter at ISO 6).