It's never going to be 100% accurate, so the first thing to ask is:

Is it close enough? I don't know exactly how close it can get, since I don't use a treadmill, but I'm happy with <10% off. The biggest reason to get your stride length correct - in my opinion - is so that FitBit will get its calorie calculation correct. So, don't fret over small differences.

If you're consistently off (i.e. always short or always long, as you indicate), you could try tweaking it. Rather than going through the procedure again, just increase or decrease the stride length by small amounts (0.1 inch) - with several treadmill sessions after each adjustment - until it is close enough. (This isn't an officially sanctioned procedure, just what I think I would try.)

And, don't be surprised if it changes in the future. As I walk more, I think - I know - my stride length is changing.

I use Map My Walk and occasionally try to check my stride length against it. Yesterday was pretty good. MMW said 3.51 miles, FitBit said 3.28 miles, so off by 6.5%.

Usually the walking would tend to go the other way in wrong distance.
Device would read shorter than actual walking at exercise pace for say the 1 hr daily, but then be a tad longer for the other hours of the day, which could have equal distance.

That's why the instructions say to pick a pace between exercise level and daily strolling level. The device can adjust for most a decent amount.

Now running should just be done at normal pace, or if you vary a lot, an average pace. As Nancy mentioned, both may indeed change as body shape/weight changes.

Here's my run last weekend, which was actually jogging and walking intervals (as recovery after bike ride).
The activity record is what Fitbit had as stats.
The logged workout is what I put in.