I think your confusion is in the moment of interpreting when the mouse pointer entered the widget or left the widget. Instead of Motion let's use for example Leave and Enter events to better understand what happens.
I have taken the liberty of including some labels that show which widget we enter and left at each moment.
from tkinter import *
def test_enter(event):
enter.set(event.widget)
def test_left(event):
left.set(event.widget)
window = Tk()
window.geometry("300x300")
window.bind("<Enter>", test_enter)
window.bind("<Leave>", test_left)
frame = Frame(window, bg="red", width=200, height=200)
frame.pack()
frame.bind("<Enter>", test_enter)
frame.bind("<Leave>", test_left)
label1 = Label(frame, text="Enter")
label1.place(relx=0.1, rely=0.4, x= 0.2, y=0.2)
enter = StringVar()
label_enter = Label(frame, textvariable=enter)
label_enter.place(relx=0.3, rely=0.4, x= 0.6, y=0.2)
label2 = Label(frame, text="Leave")
label2.place(relx=0.1, rely=0.6, x= 0.2, y=0.2)
left = StringVar()
label_left = Label(frame, textvariable=left)
label_left.place(relx=0.3, rely=0.6, x= 0.6, y=0.2)
window.mainloop()
Remember that the Frame is inside the Window. I mean that when you enter the Window you have not left root Window, you will continue to be in Window. Or if you enter inside a Label you have not left the Frame.