Nice one!

A couple of enhancements:

- No need of JPG's

- Width, height, and colours are customisable

- Yellow transparent window is placed at the cursor position

- Pink window is placed close to the yellow one

- No icons in the task bar re. the 2 transparent windows

#i::
    CoordMode, Mouse, Screen
    MouseGetPos, x0, y0
    
    Gui, New
    Gui, +LastFound +AlwaysOnTop +Owner
    WinSet, Transparent, 50
    Gui, +LastFound -Caption
    Gui, Color, FFFF00 ; yellow
    Gui, Show, W250 H30 X%x0% Y%y0%
    
    Gui, New
    Gui, +LastFound +AlwaysOnTop +Owner
    WinSet, Transparent, 50
    Gui, +LastFound -Caption
    Gui, Color, FF00FF ; pink
    x0+= 100
    y0+= 10
    Gui, Show, W250 H30 X%x0% Y%y0%
return

I added "+Resize" so that you adjust the size of the box to match the length of the sentence clause you are looking at

#i::
CoordMode, Mouse, Screen
MouseGetPos, x0, y0

Gui, New
Gui, +LastFound +AlwaysOnTop +Owner
WinSet, Transparent, 75
Gui, +LastFound -Caption +Resize
Gui, Color, FFFF00 ; yellow
Gui, Show, W250 H30 X%x0% Y%y0%

Gui, New
Gui, +LastFound +AlwaysOnTop +Owner
WinSet, Transparent, 75
Gui, +LastFound -Caption +Resize
Gui, Color, FF00FF ; pink
x0+= 100
y0+= 10
Gui, Show, W250 H30 X%x0% Y%y0%
return

Yeah, but there is visible little title bar on the top of each window. I’m sure it can be removed, but no time to check now.

This is a way to make variable length highlights without any border.

With this, you can make as many boxes as you like so it essentially gives you a highlighter pen you can use anywhere on the screen. 

Additional highlighter colours could be done with additional hotkeys as required.

There is probably a way to "toggle" the code so that one hotkey could be used for both the start and end points but I am not smart enough to figure it out.

CoordMode, Mouse, Screen

F5::
global startxpos
global startypos
MouseGetPos, startxpos, startypos
return

F6::
MouseGetPos, endxpos, endypos
boxw:=endxpos-startxpos
boxh:=20
boxy:=startypos-10
Gui, New
Gui, +LastFound +AlwaysOnTop +Owner
WinSet, Transparent, 75
Gui, +LastFound -Caption -Border ToolWindow
Gui, Color, FF00FF
Gui, Show, W%boxw% H%boxh% X%startxpos% Y%boxy%
return

F4::reload

This is a way to make variable length highlights without any border.

With this, you can make as many boxes as you like so it essentially gives you a highlighter pen you can use anywhere on the screen. 

Additional highlighter colours could be done with additional hotkeys as required.

There is probably a way to "toggle" the code so that one hotkey could be used for both the start and end points but I am not smart enough to figure it out.

CoordMode, Mouse, Screen

F5::
global startxpos
global startypos
MouseGetPos, startxpos, startypos
return

F6::
MouseGetPos, endxpos, endypos
boxw:=endxpos-startxpos
boxh:=20
boxy:=startypos-10
Gui, New
Gui, +LastFound +AlwaysOnTop +Owner
WinSet, Transparent, 75
Gui, +LastFound -Caption -Border ToolWindow
Gui, Color, FF00FF
Gui, Show, W%boxw% H%boxh% X%startxpos% Y%boxy%
return

F4::reload

Good!

I think that dragging the window border seems more natural to me, but I give you and idea re. using only 1 hotkey:

There is a message box with a 4-seconds timer. That's the time you can use to move the mouse to the second point of the highlighter. When timer triggers, actual mouse position is saved as the second point.

If you press ENTER with your keyboard, the script works as well.

If you press CANCEL key or Cancel button, the script is cancelled and no highlighter is drawn.

If you press OK button with the mouse, the result probably won't be the desired one...

CoordMode, Mouse, Screen
F6::
    MouseGetPos, startxpos, startypos
    MsgBox, 33, Set the 2nd point of the highlighter window,Now move horizontally the mouse to the 2nd point of the highlighter window.,4
    
    IfMsgBox, Cancel
        return
    
    MouseGetPos, endxpos, endypos
    boxw:=endxpos-startxpos
    boxh:=20
    boxy:=startypos-10
    Gui, New
    Gui, +LastFound +AlwaysOnTop +Owner
    WinSet, Transparent, 75
    Gui, +LastFound -Caption -Border ToolWindow
    Gui, Color, FF00FF
    Gui, Show, W%boxw% H%boxh% X%startxpos% Y%boxy%
return

Thank you!

I replaced the message box with sleep, 1000

I made quite a few improvements

AutoHotKey Highlighter Pen Tool (Software applications) (proz.com)