It looks like you have a very lovely home! The mismatched floors would not bother me in the least. I love homes that are unique rather than looking like they came from Pottery Barn, RH, etc.

If at some point they really bother you then you can make a change.

They will probably use a horizontal piece like you have now - but the area under the wall is larger than that so they may need to try to make the area between the two floors the same size and then put in horizontal strips. I see that frequently and it is not a big deal but it is an indication that there was a wall there - so are big covered beams between rooms.

You have a nice size opening which allows some connection without taking down the wall. Have a good reason to take down the wall before doing so - it may be quite expensive with little change in style of function.

This is going to be a very expensive wall removal, judging by the apparent air return in the wall and the header in the dining room bearing on the end. The floor patch/replacement will be pennies in comparison.

If the two floors were stained the same, I don't think the pegs would detract from the floor. With or without the wall, it is still two individual spaces