I am probably whistling in the wind, but could you add a preference whether you want,

1) all of the exercise calories to be eaten back
2) half of the exercise calories eaten back
3) none of the exercise calories eaten back

The reason I suggest a preference is because of the fact that you are not
deducting the resting energy expenditure time spend exercising when you "eat back" the calories.

What this means, is say i do 2 hours very low intensity work at a mets of 2 and burn 200 calories an hour for 2 hours.
This is 400 calories that the system will ask me to eat back.
However by exercising 2 hours I didn't burn 200 calories I burn normally sitting.
So not only am I eating back the calories, but I am eating back my deficit.
In fact, with a 300 cal deficit goal that I have, I would be eating back 2/3 of that deficit!
In effect, giving a 100 cal deficit. No wonder dieting is so easy!

With difference exercises and time the error will differ, but it will be an error nonetheless.
Afterburn or EPOC will vary but is incorporated into ones activity level.

Eating half the calories back makes sense as an option so that it takes the fact of not
deducting REE into account, if this system is not going to.

That is my suggestion.

You know you can adjust the amount of exercise calories that are calculated, right? Just enter your time and then tab over and change your calories burned to half of whatever was calculated. Not a perfect fix but it might do what you are asking for in the meantime!

I always wait until after all my food is entered for the day before I enter my exercise. That way, I don't have to worry about it. My deficit is what it is at that point.

Yes, there are workarounds.

I can enter less exercise than I perform or change the values.

Or wait until entering it, although I would then need to eat over the recommended amount
to get to half. Because I do generally I eat back half as pre/during/post workout nutrition.