I think the following can be adapted to suit your needs, and does not
require a stay open app...
Save this example as an app bundle named 'Wait'.
Peter B.
-----
-- some of your script
tell me to activate
display dialog "Do it now...?" buttons {"Cancel", "Wait", "OK"} default
button 3
set button_pressed to button returned of result as text
if button_pressed is "Wait" then
tell application "System Events"
set visible of application process "Wait" to false
repeat until visible of application process "Wait" is true
end repeat
end tell
end if
-- resume script on dock click
tell me to activate
display dialog "Are you sure you're ready...?" buttons {"Cancel", "OK"}
default button 2
-- rest of script
-----
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