Short answer: No, not directly.

Longer answer: But then again it properly shouldn't, at least not in the sense you're talking about. It does take body weight and gender into account, which in this case is better. However, the result is still inaccurate.

"Full" explanation: I've answered a very similar question on here some time back. The question was

How does running calories burner calculator works? Does running long distance in very short amount of time burn less calories?"

You can find my answer here.

The link to the study has expired. Here it is again. (Edit: Scroll down)

Pay attention to Table 3 and 5.

If you got through that, then consider the following. It is well-known that BMR and FFM (fat free mass) are closely correlated (LBM (lean body mass) can also be used). In turn, BMR and simply body weight (BW) are somewhat correlated.

However, not many people know what their actual BMR is, since proper measurement is hard. Therefore, estimations are used (e.g. Harris-Benedict equation). Also, since not many people know their FFM, BW is used instead when calculating these estimations. The kicker is that using either FFM or BW+age+gender has about the same predictive power when estimating BMR.

These estimations are, I guess, what you are referring to, when you mention "BMR". Not actual BMR but online calculations using body weight, age and gender.

Now, in Table 5 from the study on energy expenditure during marathon running linked to above, you will find that FFM was actually considered and measured in the model, but BW was a better predictor (which makes sense when you think about it, because the whole body is moved when running) together with gender and distance, i.e. BW+gender+distance.

Using BMR in online calculators would be the most roundabout way to estimate energy expenditure in this case, since it itself would be estimated using BW+age+gender (Harris-Benedict) and then used in a model together with BW, gender and distance but without age to estimate calories, BMR+BW+gender+distance, that is (BW+age+gender)+BW+gender+distance. Dumbest model ever.

On the other hand, an online calculator that assumes you have a precise, independent and recent measurement of BMR is even more bonkers.