Suggest don't try to use 2 plans to get to the same goal, you'll confuse youself.
Yes, they should be close, but they will always be different.
MFP is taking the daily burn figure, comparing it to your non-exercise maintenance in your profile, increasing or decreasing as needed to make it match - then taking off the deficit of say 500 for 1 lb weekly.
But until the end of day, they are both estimating total daily burn differently, so subtracting 500 on 2 estimates gives 2 different amounts.
On MFP Exercise diary, also confirm the time of last sync by clicking on the i on the adjustments.
Suggest you use one as primary, the other as tool to help the primary.
If the food logging ease on MFP is big deal (for most it is) - use that as primary, Fitbit will be tool to correct MFP's figures. So you can set Fitbit to whatever goals on diet you want - won't matter.
MFP only receives the daily burned calories to do math with.
Now - that setting you found does change what Fitbit reports up to that point in the day. If Fitbit is overestimating based on history your burn, MFP will do the math. Also turn off Calorie estimation in your personal settings if you won't be forgetting your device. That can mess up the number too.
Fitbit does some estimating until it gets the next sync, so you have most accurate reports just after a sync. In other words - don't won't to sync right before bed.
---------------------------------------------------------------------------------
Help the next searcher of answers, mark a reply as Solved if it was, or a thumbs up if it was a good idea too.
