Basically, you should be able to copy links to mod/lti/view.php and use them anywhere on the site and have the "Open in new window" launch mode work properly. This IS the case now on 4.1 and beyond, thanks to a fix to mod/lti/view.php contained in MDL-69275. We should just backport that to other branches in this issue.

To replicate:
1. Create an external tool instance in the course, making sure to set "Launch container" to "New window"
2. Launch this (you'll see a new window launch and that's normal - that's not the bug yet)
3. Now, copy the link to this activity (mod/lti/view....) and add it as a link (via Atto/Tiny) to a label resource (or whatever we're calling that now in 4.1+)
4. Now, click the link in the label you just added:
In 4.1: This now correctly still opens the tool in a new window (you'll see the activity page open with "the tool opened in a new window" or something like that.
In 4.0 and older: This will open the tool in an embedded view, which is wrong.