i don't have access to the opening explorer, but it is possible to reach the position after 5.nbd7 with a different move order. 4..nd7 5 nf3 ngf6 and you have the same position, except white did not have to blunder a knight in another line to reach it. the master games likely used this move order, and the opening explorer is probably also giving the position coming from 4..nd7.
i suspect this is also the case with bd3. the opening explorer will find a position where this can be reached, and not necessarily the one you input in that order, and then it will show which is the most played move there.
it won't make sense of course but you should just blunder check, and not trust the feature blindly.
this is the move order i am talking about. you see it reached the position both after 5 nf3 blundering the knight on e4 and also bd3 with black blundering his own knight on e4, but with this move order there are no hanging knights. so it may be suggesting the most common move from this move order, which makes sense since 4..nd7 is a main line, and there's lots of games with this move, most of them from the old pre-computer era.
Playing black, after 5.Nf3, the obvious move, and the best move according to the engine, is ..Nxe4. But in the master games explorer, the most common move by far in this position is ..Nbd7, which gives away all your advantage. Why would you not take the free knight?
So if you instead play the best move Nxe4 and white attacks your knight with Bd3, the most common move in that position is again Nd7, which makes no sense. What's going on here?