Yes even calling that script you would still get the remote deployment dos window pop open.
We rarely use the logged on user, however there are some times where it is required.
What we do is call a message beforehand advising the user that we are installing software etc and a follow message to let them know when its done.
It's not ideal, I have requested that Lansweeper implement something a little better with the software deployment, eg a little notification installation window that could be toggled.
Example: https://www.lansweeper.com/forum/yaf_postst16718_Option-to-show-surfaces-to-the-user-when-deploying-software.aspx#post56212