There is a way to get them to flash together. Just click out 5 or 6 of them in rapid succession and find the two that blink together. Move them into place and delete the rest.

I think the alternate flashing looks better and makes more sense. I hate the vanilla way all the planes blinking navigational lights blink at the same time. This helps to brake that up a bit. This asset delivers in brightness and at just the right level. Well done.